To study the effects of long-term no-tillage direct seeding mode on rice yield and the soil physiochemical property in a rice-rapeseed rotation system, a comparative experiment with a water-saving and drought-resistance rice (WDR) variety and a double low rapeseed variety as materials was conducted under no-tillage direct seeding (NTDS) mode and conventional tillage direct seeding (CTDS) mode for four years, using the CTDS mode as the control. Compared with the CTDS mode, the actual rice yield of WDR decreased by 8.10%at the first year, whereas the plant height, spikelet number per panicle, spikelet fertility, 1000-grain weight, grain yield, actual yield, and harvest index increased with no-tillage years, which led to the actual yield increase by 6.49%at the fourth year. Correlation analysis showed that the panicle length was significantly related to the actual yield of WDR. Compared with the CTDS mode in terms of the soil properties, the pH value of the NTDS mode decreased every year, whereas the contents of soil organic matter and total N of the NTDS mode increased. In the 0-5 cm layer of the NTDS mode, the soil bulk decreased, whereas the contents of soil organic matter, total N, and available N increased. In the 5-20 cm layer of the NTDS mode, the available N and K decreased, whereas the soil bulk, contents of soil organic matter, and total N increased. In summary, the NTDS mode increased the rice yield, and could improve the paddy soil fertility of the top layer.