Vegetation restoration is the most widely used forest management practice for degraded soils, but the responses of soil quality in different vegetation restoration types may vary. In addition, the relationship between water flow paths connection and soil quality needs to be further explored. In this study, the soil quality index (SQI) and the index of water flow connectivity (IWFC) in the six water flow patterns (PFP, SSB, WSB, CPS, CPW, and CSW) were explored at three forest stands (oak, pine, and bamboo forests) with 50 years for enclosure. The results showed that the bamboo forest stand had the best soil quality as a whole (0.534 ± 0.135), followed by pine (0.530 ± 0.180) and oak forest stands (0.435 ± 0.205). The IWFC in PFP, CPS and CPW water flow patterns decreased gradually with increasing soil depth, while in SSB, WSB and CSB water flow patterns, the IWFC increased at first and then decreased. Finally, the IWFC in the CPW water flow pattern showed the largest positive correlation with the SQI (P < 0.05). The IWFC in the CPW water flow pattern driven by soil physical properties could mainly control the changes in the SQI indirectly (average IE = 0.825) by influencing soil nutrient (average IE = 0.447) and biological (average IE = 0.485) properties, while its direct effects could be ignored (average DE = −0.074), which demonstrated that the joint effects of preferential flow paths and weak stream buffer zones can dramatically reflect the changes in soil quality. The better soil improvement effect of bamboo and pine forest stands compared to the oak forest stand should be given more consideration. This study provided new insights for the assessment of the relationship between soil hydrology and soil quality.