With the gradual transfer of an enormous young and middle age labor force from agricultural field to non-agricultural sectors, the negative role of land fragmentation (LF), which is related to food security, is increasingly reflecting in the process of agricultural modernization. Meanwhile, the positive roles of farmers’ combined-tillage in production are gradually emerging. Based on the above background, this study explained the relationship among farmers’ combined-tillage, LF and agricultural production efficiency (APE). The study used survey date and the SFA-QR model to empirically investigate the effects of LF and farmers’ combined-tillage on APE. Furthermore, this article analyzed the moderating effect of farmers’ combined-tillage on the relationship between LF and APE. The results demonstrated that: (1) Farmers combined-tillage improves the APE significantly, especially on low and medium efficiency households; (2) LF has a negative impact on APE, especially on low and medium efficiency households; (3) Combined-tillage could alleviate the adverse effects of LF on APE. In this regard, the paper also proposed some suggestions to face the adverse effects of LF and promote farmers’ combined-tillage in production.