To investigate the effect of nitrogen application and soil microbial activity on the decomposition process of stalk material in stalk composite pipes (SCPs) under subsurface irrigation with stalk composite pipes (SSI), in this study, a field experiment was conducted with two fertilization strategies—banding fertilization and SCP fertigation—at three nitrogen doses (126, 168, and 210 kg/ha), and the Biolog Ecoplate™ was employed to determine soil microbial activity. The results showed that under banding fertilization, the soil microbial activity at 20 cm subsoil and at the SCP wall increased with the increase in nitrogen dosage, ranging from 37.6% to 54.3% and from 21.5% to 23.7%, respectively. Under SCP fertigation, the soil microbial activity at 20 cm subsoil first showed a 58% surge, followed by a 3.9% decrease, with no significant variation in soil microbial activity at the SCP wall. Forty-five days later, the crude fiber content in the SCP wall under SCP fertigation was 17.6–26.3% lower than that under banding fertilization. Based on the comprehensive analysis of the soil microbial activity, SCP fertigation combined with high nitrogen application can accelerate the decay rate of straw in SCPs. This research can provide a reference for formulating irrigation and fertilization regimes for SSI.