Manure and chemical fertilizers have different effects on soil properties, the nitrogen cycle, and crop yield. This study aimed to investigate the effects of different fertilizer applications under the same N input on soil physicochemical properties and soil bacterial communities and to explain the contributions of soil properties to grain yield. Manure substitution of chemical fertilizer was conducted in leaching monitoring systems. The study began in 2009 and sampling was carried out in 2014 and 2016. Three fertilizer treatments with the same total N, P, and K application rates and one control treatment were designed as follows: (1) CK, without nitrogen fertilizer; (2) 100%U, whole nitrogen coming from urea; (3) 100%M, whole nitrogen coming from composted cattle manure; and (4) 50%U + 50%M, half nitrogen from composted cattle manure and half nitrogen from urea. Soil organic carbon (SOC) content was positively correlated with total N (TN), NO3−–N, and NH4+–N contents, the mean weight diameter of soil aggregates, and the Shannon diversity index of bacteria, whereas SOC content was not significantly correlated with grain yield. NO3−–N content was positively correlated with grain yield. Substituting half the amount of chemical fertilizer with manure as a nitrogen source improved soil stability, increased bacterial diversity, and enhanced nitrogen supply, while reducing nitrogen loss from ammonia volatilization and nitrogen leaching. Substituting half the amount of chemical fertilizer with manure as a nitrogen source was a more sustainable way to increase grain yield through a sustainable nitrate supply and to reduce N loss.