Plant roots show morphological plasticity to adapt to heterogeneous nitrogen (N) and phosphorus (P) distribution, but how fertilizer placement affects root growth and nutrient uptake of perennial non-herbaceous species (including Rosa multiflora Thunb. ex Murr. that was the subject of this study) is not understood. A pot experiment was conducted with five N and five P fertilization rates to determine the appropriate application rates. Then, a soil column trial (using the selected N and P rates) was conducted with four placements, including N and P applied alone or in combination to either 0–15 cm or 15–30 cm soil layer, and NP mixed throughout the soil as the control. The results showed that the application rates of 80 mg N kg−1 and 80 mg P kg−1 soil were appropriate for root growth and trunk expansion of Rosa multiflora. Deep banding of NP in the 15–30 cm soil layer increased the first-order lateral root length and density in the fertilized zone as well as P accumulation compared with the NP mixed and the other placement treatments after 46 days. After 108 days, compared with the NP mixed treatment, total plant N and P accumulation significantly increased in the deep NP banding treatment, with decreased rhizosphere pH and improved root growth in the deep fertilized zone; however, similar or significantly decreased plant N and P accumulation was observed in the other three placement treatments. These findings indicated that deep banding of NP in the 15–30 cm soil layer significantly stimulated root proliferation and improved root spatial distribution, which can be an effective management strategy for optimizing Rosa multiflora growth and nutrient uptake.