The in situ 120 days experiment was conducted to investigate effects of rainfall on nitrogen and phosphorus loss from courtyard composting with four kinds of coverage, involving no coverage, rice straw, thin film and soil, and their risks of nonpoint source pollution were discussed. The results showed that, with decomposing of the manure and increasing of runoff, the concentration of total nitrogen (TN), ammoniac nitrogen (NH4(+)-N), nitrate nitrogen (NO3(-)-N), total phosphorus (TP) and dissolved phosphorus (DP) from courtyard composting decreased. Especially, the concentration variation of TN, NH4(+)-N, NO3(-)-N with time fit for I kinetic equation, while TP and DP fit for linear equation. The concentration order of nitrogen and phosphorus in runoff observed as follows: no coverage > coverage by rice straw > coverage by soil > coverage by thin film. As a result, the coverage by thin film could be used as a recommended mode to decrease the loss of nitrogen and phosphorus in runoff resulting from its low risks for nonpoint source pollution.