Paddy-upland rotation is the main cropping system in the irrigation area of the Western Sichuan Plain. In order to investigate the effects of different paddy-upland rotations on the annual soil respiration in this region, static chamber-gas chromatography was used to measure the soil respiration of garlic-rice (GR), wheat-rice (WR), and rape-rice (RR) models. The hydrothermal ecological factors, including the temperature and water layer height, were determined at the same time. The results showed that the cumulative discharges of soil respiration in the three rotation models were in the order of GR > RR > WR, at 193.36, 160.27, and 157.28 kg/hm², respectively. The daily dynamics of soil respiration were basically the same; all showed the unimodal variation trend, and the highest value appeared at 12:00-15:00. The daily variation from June to August was higher than that in the other months, and the seasonal dynamics of soil respiration showed a bimodal trend, with peaks in June and September. The annual average soil respiration rate of the GR model was the highest; the soil respiration of the three models was significantly affected by soil temperature at 0-10 cm and 10-20 cm, but there was no significant correlation with soil water content. Soil temperature is the main influencing factor of seasonal variation in soil respiration in the dry season, while a combination of soil water depth and soil temperature affects the variation in soil respiration in the rice growing season.