Excessive tillage and soil compaction threaten the sustainable farmlands in the Huang-Huai-Hai Plains of China. Our study explores tillage practices to improve soil and root ecology and promote productivity in the winter wheat fields. We tested the impact of plowing, rotary, strip rotary tillage and strip rotary tillage with a two-year subsoiling interval (SRS) on wheat yield and root quality. SRS decreased soil bulk density compared with other treatments, resulting in lower soil penetration resistance. Root morphology and weight density decreased with the increased soil depth and was higher in SRS. Moreover, SRS increased the indoleacetic acid and trans zeatin riboside levels corresponding to greater TTC reduction activities, the total and active absorption root area. SRS increased the superoxide dismutase and catalase activities and soluble protein concentration and decreased the malondialdehyde concentration. The first two factors extracted using 11 root attributes in various soil layers through principal component analysis were selected as the integrated indicators for the minimum data set, and their integrated score was calculated to quantify the root quality. Our study suggests that SRS could significantly improve root morphology and enhance the root activity in subsoil layers, thus, delaying root senescence and increasing winter wheat yield.