Objectives To address the existing uncertainty regarding the optimal organic manure substitution rate for achieving multi-objective synergy in the potato-wheat rotation system in Yunnan Province, this study adopted an integrated machine learning framework combining Gaussian Process Regression (GPR), NSGA-Ⅱ multi-objective optimization algorithm, and TOPSIS multi-attribute decision-making method, to identify a fertilization strategy that integrates chemical fertilizer reduction with organic amendment application, so as to simultaneously improve fertilizer use efficiency and soil fertility.

Methods A consecutive three-year field experiment was carried out from 2023 to 2025 in the representative potato-wheat rotation region of Yunnan Province. Farmers’ conventional fertilization practice (FP) served as the control, and treatments included recommended fertilization by nutrient expert system (NE), organic manure substituting 20% (M20), 40% (M40), and 60% (M60) based on the NE recommendation, alongside zero-nitrogen, zero-phosphorus, and zero-potassium treatments. Variations in crop yield, nutrient uptake, soil physicochemical properties, soil microbial biomass, and soil enzyme activities were analyzed. The NSGA-II and TOPSIS models were applied to evaluate comprehensive multi-objective benefits.

Results Organic substitution treatments (M20-M60) based on optimized fertilization increased crop yields. Compared with the FP treatment, potato and wheat yields increased on average by 8.6%-10.3% and 7.5%-11.8%, respectively. Potato yield increased by 6.0%-7.5% compared with the NE treatment, whereas wheat yield showed no significant difference when averaged over the two years. Optimized fertilization with organic substitution significantly enhanced crop nutrient uptake and significantly improved fertilizer use efficiency through increased biomass accumulation and soil fertility enhancement. Specifically, nitrogen recovery efficiency (REN) under M20 and M40 increased by 7.9 and 10.0 percentage points compared with FP, and by 1.8 and 3.9 percentage points compared with NE, respectively. The effects of organic substitution rate on soil physicochemical properties varied: soil mineral nitrogen (Nmin), available phosphorus (AP), and available potassium (AK) tended to decrease with increasing substitution rate, yet values under M20 were 10.7%, 11.4%, and 10.7% higher than those under NE, respectively. Compared with NE, organic substitution treatments increased soil organic matter (OM) content, with M40 showing the greatest improvement (an average annual increase of 6.5%). Compared with FP, M20 treatment significantly increased the contents of mineral-associated organic carbon and nitrogen (MAOC/MAON), whereas M40 treatment was most effective in enhancing soil particulate organic carbon (POC) and microbial biomass; in contrast, a high substitution ratio (M60) had negative effects on microbial biomass. Furthermore, compared with NE, M20 significantly increased N-acetyl-β-D-glucosaminidase (NAG) activity by 56.6%, M40 significantly increased β-cellobiosidase (CB) activity by 56.5%, and M60 significantly increased phosphatase (PHOS) activity by 49.8%. Based on NSGA-II and TOPSIS modeling simulations using plant balance index, enzyme activity index, and soil balance index as objectives, the optimal organic substitution rate for the potato-wheat rotation system in Yunnan was determined to be 25% on the basis of NE fertilization. This optimal rate is projected to increase annual yield by 6.4%, improve REN by 2.5 percentage points, and increase soil OM by 5.4% annually compared with NE.

Conclusions In the potato-wheat rotation system of Yunnan, rational organic substitution under optimized fertilization improved soil labile organic carbon and nitrogen pool fractions, microbial biomass and extracellular enzyme activities, significantly enhanced nutrient uptake, and increased potato and wheat yields. Maintaining an organic manure substitution rate for chemical nitrogen between 23.8% and 29.3% facilitates improvements in crop yield, fertilizer use efficiency, and soil organic matter content. This range represents an appropriate fertilization strategy for the region, providing key technical parameters to support efficient nutrient utilization and non-point source pollution mitigation in local agricultural production.