· The soil pathogen-induced Janzen-Connell (JC) effect is considered as a primary mechanism regulating plant biodiversity worldwide. As predicted by the framework of the classic plant disease triangle, severity of plant diseases is often influenced by temperature, yet there is little understanding of how increasing temperatures may affect the JC effect, hampering predicting the impact of global warming on biodiversity.· We conducted a three-year field warming experiment, using open-top chambers with fungicide treatment, to test the effect of elevated temperature on seedling mortality of a temperate tree species, Prunus padus, from a genus with known susceptibility to soil pathogens.· The results showed that the elevated temperature significantly increased mortality of P. padus seedlings at the immediate vicinity of parent trees, concurrent with the warming increased relative abundance of pathogenic fungi identified to be virulent to Prunus species.· Our study offers the first of its kind experimental evidence suggesting that global warming significantly intensify the JC effect on the temperate tree species due to the increased relative abundance of pathogenic fungi. This work advances our understanding about changes of the JC effect to the ongoing global warming, which has important implications for predicting tree diversity in the temperate in a warmer future.