Objectives Soil salinization is one of the major constraints limiting nutrient-use efficiency and crop productivity in the winter wheat-summer maize rotation system of the North China Plain. A long-term field experiment was conducted to investigate the effects of different application amounts of humic acid (HA) on the amelioration of saline-alkali cropland and on nutrient uptake and utilization in the winter wheat-summer maize rotation system, so as to provide a scientific HA dosage.

Methods A two-year located field experiment was conducted from 2023 to 2025 in a moderately to severely saline-alkali farmland in Wucheng County, Shandong Province. Seven HA application rate treatments were established, including: 0, 750, 1500, 3000, 4500, 7500, and 15000. kg/hm², denoted as CK, T1, T2, T3, T4, T5 and T6 in turn. The crop yield, partial factor productivity (PFP) of N, P, and K fertilizers, basic soil salinity properties, and the contents of water-soluble ions and microbial communities were analyzed at each harvest.

Results The application of HA significantly increased the crop yield in the winter wheat-summer maize rotation system. The PFP of N, P and K fertilizers in both winter wheat and summer maize seasons under T5 and T6 treatments was significantly improved, increasing by 44.91% to 66.91% compared with CK. Among them, the PFP of N, P and K fertilizers in the 2025 summer maize season was the highest under T5 treatment, while in the other seasons, T6 showed a slightly higher value but the difference from T5 was not significant. HA application gradually reduced the total soil salt content and the contents of water-soluble ions such as Na⁺, Cl⁻ and SO₄²⁻, while synchronously increasing the contents of water-soluble ions including K⁺, Ca²⁺ and Mg²⁺. The salt-reducing and quality-improving effect accumulated year by year with the extension of application years. HA also significantly enhanced the diversity of soil bacterial and fungal communities, and directionally enriched functional flora involved in nitrogen and phosphorus transformation such as as Proteobacteria, Bacteroidota and Ascomycota, among which T5 treatment showed the most prominent regulatory effect on the microbial community structure.

Conclusions Continuous application of humic acid can effectively reduce the total soil salt content and the concentrations of water-soluble ions including Na⁺, Cl⁻ and SO₄²⁻, while increasing the contents of water-soluble Ca²⁺, Mg²⁺, K⁺ and other ions. It also elevates the diversity of soil bacterial and fungal communities, directionally enriches N and P transformation functional flora such as Proteobacteria, Bacteroidota and Ascomycota, and optimizes the soil micro-ecological environment. This further improves the crop yield and the partial factor productivity of N, P and K fertilizers in the winter wheat-summer maize rotation system. The humic acid application rate required to achieve stable desalination and soil improvement effect is 7500 kg/hm².