Soil respiration is an important pathway of carbon release from the terrestrial biosphere to the atmosphere, which plays a key role in ecosystem carbon cycling. However, the response and mechanism of soil respiration to nitrogen and phosphorus addition in legume plants are still unclear. Here, a pot experiment planted with soybean (Glycine max (L.) Merr.) was conducted to investigate the effects of nitrogen (N) and phosphorus (P) addition on soil respiration. Four treatments were designed: control, N addition, P addition, and both N and P addition. Soil respiration was measured twice a month from June to September in 2022. Our results showed that nutrient addition treatments presented significantly negative effects on soil respiration. In particular, nitrogen addition not only directly affected soil respiration, but also indirectly impacted soil respiration by altering soil nitrate nitrogen content. Elevated soil nitrate nitrogen content could inhibit soybean root nodule number and reduce biomass allocation to roots, thereby decreasing soil respiration. Furthermore, phosphorus addition and nitrogen–phosphorus co-addition strongly inhibited soybean nodulation by changing soil pH value, thus inhibiting soil respiration of soybean. The findings provide baseline information for optimizing nutrient management in legume crops.