Both PU and PC increased maize yield, water use efficiency (WUE), and partial factor productivity from applied N (PFPN), relative to CK. PC increased maize yield more than PU, and had higher soil organic carbon (SOC) content than PU, which was mainly due to the decline in SOC stocks in the 250–2000, 53–250, and <53 μm soil aggregates. The soil bacterial community structure was driven by SOC, C: N ratio, total nitrogen (TN), pH, microaggregates, clay and silt in CK, and by larger macroaggregates and mean weight diameter in PC and PU. Both PC and PU significantly changed soil bacterial community beta diversity, and decreased both positive and negative links of the co-occurrence network, relative to CK. Better soil nutrient conditions in PC explained the small number of positive and negative links between soil bacteria. Our results suggest PM improves maize yield, water and nitrogen use efficiency, and soil aggregate stability while alleviating bacterial competition. However, the reduction of SOC and pH caused by PM still needs our attention. PC alleviates the decline of soil fertility and soil acidification and has higher yield relative to PU. Therefore, we proposed PC is a potential agricultural measure that can replace PU on the Loess Plateau.