Biochar is widely used in agriculture to enhance crop yield, improve soil fertility, and regulate greenhouse gas (GHG) emissions. Its effectiveness, however, depends not only on its properties but also on soil moisture conditions, making integrated water management essential for maximizing its benefits. The study reports the results of a laboratory incubation experiment using three biochar application rates (0, 20, and 40 t ha−1) and two irrigation regimes—flooded irrigation and alternate wetting and drying (AWD)—to investigate the effects of biochar amendment and water management on soil greenhouse gas (GHG) emissions. The results indicated that there was no significant interaction between biochar and water regulation on GHG emissions, and changes in soil moisture and biochar application levels had no significant impact on carbon dioxide (CO2) emissions. Compared to flooded irrigation, AWD effectively enhanced soil microbial activity, increasing nitrous oxide (N2O) emissions by 62.50% to 88.35%, but significantly reducing methane (CH4) emissions by 44.30% to 68.55%, thereby lowering the soil’s global warming potential (GWP). Additionally, biochar amendment significantly increased soil SOC and TN contents, enhanced soil enzyme activities, and significantly improved microbial carbon use efficiency (CUE), the C/N ratio, and the net nitrification rate (NNR). However, it had no significant effect on soil N2O and CO2 emissions, while significantly suppressed CH4 emissions. Throughout the entire growth period, biochar application increased soil GWP overall. However, during the first water cycle, GWP increased with higher biochar application rates, whereas in the second water cycle, biochar application exhibited a suppressive effect on GWP. In conclusion, integrating biochar application with AWD irrigation can optimize soil CUE, enhance soil nutrient supply, and mitigate, to some extent, the potential increase in GHG emissions induced by biochar. This provides valuable insights for carbon management and sustainable agricultural development.