The supposition that cropping system might affect fertilization-induced changes in chemical composition of soil organic carbon (SOC) and microbial community composition has mostly derived from field experiments in different sites, which may have been disturbed by different climate conditions and parent materials. Here, two adjacent long-term field experiments were used, which contained similar four fertilization regimes of NPK, 2NPK, NPKOM, and an unamended control (Control), while contrasting annual cropping system of rice–rice and maize–maize, to investigate how fertilization-induced changes in SOC chemistry differ in paddy soil from upland soil, and whether they correlate with different bacterial taxa. The bacterial community composition of the paddy soil was mainly determined by NO3–-N and total N, and that of the upland was mostly explained by SOC. The NPK, 2NPK, and NPKOM treatments from the paddy soil increased CCH3, decreased OCH, and reduced CH/CH2, while those from the upland soil decreased CH/CH2, increased OCH, and raised CH/CH2, respectively, indicating opposite shifts of OCH and alkyl C (i.e., CCH3 and CH/CH2) in each paired fertilizer treatment of the two soils. In the paddy soil, the CCH3 from the NPK treatment showed no association with any bacterial taxa, the OCH from the 2NPK showed a negative association with NO3–-related species, and the CH/CH2 from the NPKOM showed a negative association with Proteobacteria and Bacteroidetes. In the upland soil, the CH/CH2 from the NPK negatively associated with Thermogemmatisporales and Acidobacteriaceae subgroup 1, the OCH from the 2NPK positively associated with Thermogemmatisporales, and the CH/CH2 from the NPKOM positively associated with copiotrophic bacterial taxa. Our results provided direct evidence that cropping system mediated the shift direction of specific functional group under specific fertilization regimes, and implied that completely opposite shifts of OCH and alkyl C in each paired fertilizer treatment of the paddy soil and upland soil can likely be attributed to different fertilization-induced shifts in the microbial community composition resulting from soil N change in the paddy soil and soil C change in the upland soil.