Low temperature has negative effects on apple photosynthesis by inhibiting the accumulations of photosynthates and nitrogen. The interactive effects of low temperature and nitrogen application on photosynthetic parameters and the absorption and distribution of carbon and nitrogen in different organs were assessed to investigate if nitrogen application can relieve the low-temperature stress on gas exchange and the accumulations of carbon and nitrogen inside the apple plants. No matter under normal or low-temperature conditions, nitrogen application both improved the photosynthetic parameters including net photosynthetic rate, intercellular CO2 concentration, and quantum yield of regulated energy dissipation of PSII as well as the absorption of carbon and nitrogen in roots, stems, and leaves. Thus, we conclude that nitrogen application can relieve the effects of low-temperature stress on photosynthesis and is of benefit for the accumulations of carbon and nitrogen in multiple organs of apple seedlings.