Reducing the possibility of a potential phosphorus (P) resource crisis and increasing P use efficiency (PUE) by improving P fertilizer management is of paramount importance for truly sustainable agricultural production. However, information on how layered application of phosphate fertilizer at different soil depths affects yield and PUE in winter wheat (Triticum aestivum L.) is limited. Here, a 2-year field experiment was conducted in Gleyic Luvisols (ISSS, Isric, F.A.O, 1998) soil to compare the effects of surface fertilization (0–8 cm) with those of layered fertilization (LF) treatments including, uniform layered fertilization (1:1:1), elliptical layered fertilization (1:2:1), and trapezoidal layered fertilization (1:2:3), at soil depths of 0–8, 8–16, and 16–24 cm, on the spatial distribution of roots in different soil layers, and P accumulation at different growth stages of winter wheat in the 2016–2017 and 2017–2018 growing seasons. Our results showed that, compared with surface fertilization, all the LF treatments significantly increased yield by 6.3–20.6% and PUE by 4.7–11.2% points. Furthermore, elliptical layered fertilization resulted in the highest yield and PUE rate. The LF treatments effectively reduced topsoil (0–8 cm) root distribution by 10.8–14.7%, and increased deep-soil (8–100 cm) root distribution by 14.7–21.1% compared with surface fertilization. Linear regression analysis indicated that available P at 0–8 and 8–16 cm soil depths significantly correlated with yield. Additionally, results of structural equation modeling showed that available P at soil depths of 0–8, 8–16, and 16–24 cm had a significant positive effect on root morphology, but only at the 8–16 cm soil layer did available P have a significant positive effect on P accumulation of winter wheat. Overall, our findings suggest that elliptical layered fertilization effectively increased yield and PUE by promoting root proliferation and P accumulation in winter wheat.