Rice-winter rapeseed rotation is one of the central double-crop systems in the Yangtze River (YRB) Basin, and most soils in this region are poorly drained clay soils, which has a negative effect on rapeseed growth. A field study comprising of two different tillage depths, topsoil tillage (Top-T), and subsoil tillage (Sub-T) were conducted in the paddy field (PF) and dryland (DL) in the rapeseed season, and no-tillage (NT) in subsequent rice and soybean season. The soil properties, root-shoot growth of rapeseed, and the yield of the three crops were collected to evaluate the effects of these tillage modes. Sub-T significantly reduced soil bulk density (SBD) and penetration resistance (PR) in PF and DL, while it increased the pH in PF, the concentration of moisture and total nitrogen, organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium in the 10−30 cm soil layers, and the activities of catalase, sucrose, urease, and acid phosphatase in the 10−20 cm soil as compared with Top-T. Furthermore, Sub-T significantly enhanced root bleeding sap (RBS), indole acetic acid, cytokinin, zeatin, and gibberellin concentration but decreased abscisic acid concentration. A principal component analysis showed that Sub-T could improve RBS and root hormones and promote the biomass accumulation of root and shoot by reducing SBD and PR and increasing nutrients in 10−30 cm soil. Finally, Sub-T significantly increased the seed yield of rapeseed by 2–16.5 % and did not have any significant negative effect on rice and soybean yield under NT in the next season, whereas, the rapeseed yield was significantly reduced by 22.9–36.2 % under Top-T, the rice, and soybean yield were significantly reduced by 33.6–41.1 % and by 26.0–41.9 % under NT in the next season, respectively, when compared to those under conventional tillage (CT, involved moldboard plowing to 15−18 cm and rotary tillage to 10−15 cm). Consequently, favorable soil conditions provided by Sub-T lasted for the next season, as rapeseed growth and grain yield were significantly promoted, and both the rice and soybean yield can also be maintained under NT.