This paper investigates the effect of phosphorus on nitrogen migration and transformation during the sewage purification processes in deep subsurface wastewater infiltration systems. Good performance was achieved with a hydraulic loading rate of 0.1 m3/m2·d, indicating that the effluent water quality could meet the primary grade A values as put forth by the ‘Cities Sewage Treatment Plant Pollutant Discharge Standard’ (GB18918-2002). In addition, the results of three inflow total phosphorus (TP) concentrations (5 mg L−1, 15 mg L−1, and 30 mg L−1) indicated that high-levels of phosphorus were more advantageous in regards to improving the activity of denitrifying bacteria in soil and strengthening the effect of nitrogen removal, suggesting that the effluent total nitrogen (TN) concentration could meet the primary grade A standard (TN ≤ 15 mg L−1). It was further observed that soil depth was less crucial when inflow TP concentrations were higher. Therefore, the results indicated that inflow phosphorus concentrations could greatly influence nitrogen migration and transformation in deep subsurface wastewater infiltration systems.