It remains uncertain how tree seedling’s growth and its related physiological characteristics with different drought-tolerances respond to warming and associated inter-annual changes in precipitation. Herein, using a 2-year infrared radiation (IR) heating system in temperate secondary forests of Northeast China, we showed divergent responses of the photosynthetic properties, autioxidant enzyme activities and growth of two main tree species to warming with different precipitation levels. Compared with control, IR caused +2 °C and +1.77 °C above ambient temperature of 0-10 cm soil layer and 0.2 m above surface (seedlings’ height), and decreased air relative humidity (RH) at a height of 0.2 m by 7.51%. In the non-drought year, warming reduced photosystem II performance in two species, but significantly increased malondialdehyde (representing lipid peroxidation) content by 67% of Fraxinus mandshurica (drought-intolerant species) seedlings. In drought year, warming reduced the net photosynthetic rate of Quercus mongolica (drought-tolerant species) and F. mandschurica by 12% and 28%, and antioxidant enzyme activity for both species. The growth of Q. mongolica was not impacted by warming in the non-drought year. Warming strongly reduced the total biomass, the increasement in root collar and height of F. mandshurica in two years (by 33%, 48% and 67% in drought year, while by 30.1%, 18.4% and 10.6% in non-drought year). In addition, among the environmental factors caused by IR, RH mainly affected growth and physiology of seedlings. Therefore, the warming effect is species-specific, and the drought-intolerant species is more sensitive to projected climate change and its warming response is deteriorate with drought.