Erosion of denuded steep rocky slopes causes increasing losses of nitrogen and phosphorus, which is a severe problem in rocky slope protection. Thus, it is important to determine the appropriate materials that can reduce the erodibility and losses of nitrogen and phosphorus of the soil. In this paper, twenty-seven simulated rainfall events were carried out in a greenhouse, in which the substrate material was artificial soil; nine types of anionic polyacrylamide (PAM) were studied, which consisted of three molecular weight (6, 12, and 18 Mg mol− 1) and three charge density (10, 20, and 30%) formulations in a 3 by 3 factorial design. The results showed that: (1) Polyacrylamide application reduced total nitrogen losses by 35.3% to 50.0% and total phosphorus losses by 34.9% to 48.0% relative to the control group. (2) The losses of total nitrogen and total phosphorus had significant correlation with the molecular weight. Besides, the losses of total phosphorus, particulate-bound phosphorus and inorganic nitrogen (NH4–N) were significantly correlated with their molecular weight and charge density. However, the losses of dissolved organic nitrogen, inorganic nitrogen (NO3–N), dissolved organic phosphorus, inorganic phosphorus (PO4–P) were non-significantly correlated with molecular weight and charge density. (3) Particulate-bound nitrogen and phosphorus were responsible for the losses of nitrogen and phosphorus during runoff events, where particulate-bound nitrogen made up 71.7% to 73.2% of total nitrogen losses, and particulate-bound phosphorus made up 82.3% to 85.2% of total phosphorus losses. (4) Polyacrylamide treatments increased water-stable aggregates content by 32.3% to 59.1%, total porosity by 11.3% to 49.0%, final infiltrative rate by 41.3% to 72.5%, and reduced soil erosion by 18.9% to 39.8% compared with the control group. Overall, the results of this study indicated that polyacrylamide application in the steep rocky slope stabilization projects could significantly reduce nutrient losses and soil erosion of substrate material.