The effect of fallow tillage practices such as subsoiling and deep plowing on soil water storage and grain yields of dryland wheat has been frequently studied. However, the layered characteristics of water storage and their correlations with yield formation under each tillage were less investigated across several years. A randomized complete block design was conducted to investigate the effects of three tillage practices (NT, no-tillage; SS, subsoiling; DP, deep plowing) on soil water storage (SWS), yield structure, precipitation use efficiency (PUE), water use efficiency (WUE) and grain quality of dryland wheat for three consecutive years. The use of SS and DP increased SWS of 0–200 cm soil depths by 3.1% and 7.9% compared with NT over the 3 years. Subsoiling was more favorable for SWS in the 100–200 cm sublayer, while DP strongly increased the effect on the 0–100 cm upper layer. The grain yields, PUEs and WUEs under SS and DP were greater than those in NT. Grain yield had great correlation with SWS0-100cm. Protein content and most grain quality indicators under SS and DP decreased. Grain qualities exhibited the most negative correlation with SWS at the sowing stage and precipitation in fallow period.