Rain‐fed rice (Oryza sativa L.)–wheat (Triticum aestivum L.) (RFRW) rotation can be a resource‐saving solution for sustainable cropping systems. However, conventional puddled and flood transplanted rice, repeat tractor compaction, and years of shallow rotary tillage and paddy–dryland rotation had a negative impact on soil physical in the RFRW rotation (e.g., soil consolidation and shrinkage, shallow tillage layer). A 4‐yr field experiment was established to determine if different post‐paddy tillage systems would improve soil physical properties and plant factors. We compared no‐tillage (NT), conventional rotary tillage (RT), and deep tillage (DT) to improve the deteriorated soil structure, soil water, wheat root system, and grain yield. The results indicated that DT increased the average soil water content by 7.25% and 9.98%, increased field capacity by 9.58 and 5.23%, and decreased the soil bulk density by 6.2 and 2.2% at 0‐to‐20‐cm soil depth in 4 yr as compared to NT and RT, respectively. The NT increased the average relative soil moisture and had higher soil bulk density at 0‐to‐20‐cm depth. The DT deepened the root growth and increased the total root point numbers by 21.0 and 22.8% at 0‐to‐40‐cm soil depth in 4 yr, respectively, compared with NT and RT. In 4 yr, the DT significantly achieved higher average grain yield by 5.3 and 13.5%, respectively, compared with NT and RT. Overall, DT after rice was shown to be a promising management approach for improving wheat yields and might enable sustainable intensification of RFRW rotation.