Objectives Crop grain yields are greatly affected by carbon sequestration and water holding capacity of farmland which are significantly influenced by different tillage measures. Comparison of these effects will provide a reference for selecting suitable tillage method in the area.

Methods A long-term experiment of conservation tillage had lasted for 12 consecutive years since 2002, the cropping system was winter wheat–summer maize rotation, and total wheat and maize straws were crushed to 3–5 cm length and returned to the soil every year. Four tillage methods were set up for the experiment, as traditional tillage, subsoling, rotary tillage and zero tillage. Soil organic carbon content, soil water content, yield and equivalent yield at different crop growth stages were measured in 2015–2016, and soil carbon storage and water storage were analyzed at the same time.

Results Tillage modes had significant (P < 0.05) effect on soil organic carbon contents, subsoiling and zero tillage could significantly increase organic carbon contents at 0–10 cm soil layer (P < 0.05), and the subsoiling effect was the most significant. At 10–20 cm soil layer, compared with the conventional tillage, the zero tillage and rotary tillage reduced soil organic carbon contents. Subsoiling significantly (P < 0.05) increased soil organic carbon content compared with the conventional tillage in wheat season, and there was no significant (P < 0.05) difference in maize season. Soil water contents at 0–10 cm soil layer of rotary tillage and zero tillage were higher than those of the subsoiling and conventional tillage in maize season. At 10–20 cm, soil water content of the zero tillage was higher than other three tillage measures in wheat season. The results of yield indicated that the subsoiling effectively increased the effective panicle number, grain number per spike and 1000-grain weight, and then increased grain yield and annual equivalent yield. The zero tillage significantly (P < 0.05) reduced soil organic carbon of subsoil layer (10–20 cm), and reduced grain number per spike and 1000-grain weight, which was not conducive to crop yield increase. Yield of wheat-maize and annual equivalent yield in two years were characterized by subsoiling > conventional tillage > rotary tillage > zero tillage.

Conclusions Subsoiling could effectively promote soil organic carbon accumulation and improve water retention capacity of plough layer, and increase the number of effective panicles, grain number per spike and 1000-grain weight, thus increasing yield. Besides, the carbon reserves of the surface layer (0–10 cm) and soil water holding capacity of plough layer were significantly enhanced by zero tillage.