A 3-year field research was conducted to investigate the effect of four subsoiling methods on maize yield and water use efficiency. These four subsoiling methods included bulk subsoiling in autumn (BS), annual ridge subsoiling in autumn, annual furrow subsoiling in early summer, and interannual alternate zone subsoiling (AS), which were compared with rotary tillage in spring. The results suggested that the bulk density of the soil was alternately changed by AS, but AS had limited effect on the average water storage in the soil. Overall, soil tilled by BS and AS maintained a high water-holding capacity, which could stabilize the yield of maize under varying rainfall across different years. Maize under the AS subsoiling method maintained a relatively higher production capacity and water-use efficiency compared with those under the other three types of subsoiling methods.