Studies on the CO₂ and N₂O emission patterns of agricultural soils under different ploughing practices may provide an insight into the potential and magnitude of CO₂ and N₂O mitigation in highly managed farmland soils. In this study, field measurements of soil respiration and N₂O flux with different ploughing depths were performed in the 2003–04 wheat (Triticum aestivum L.), 2004 maize (Zea mays L.), and 2004–05 wheat seasons. Soil temperature and moisture were simultaneously measured. Results showed that, in each cropping season, the seasonal variation in soil respiration developed with a similar pattern for different treatments, which was primarily regulated by soil temperature. This work demonstrates that ploughing depth can influence long-term loss of carbon from soil, but this was contingent on preceding cropping types. Given the same preceding cropping practice, no significant difference in N₂O emission was found among different ploughing depths in each cropping season.