Interactions between the decline of Mongolian pine woodlands and fungal communities and invasive pests in northeast China, are poorly understood. In this study, we investigated the fungal communities occurring in healthy uninfested, unhealthy uninfested and Sirex noctilio infested Mongolian pine and analyzed the relationship between the decline of Mongolian pine and fungal communities and woodwasp. The population number of S. noctilio was very high in the declining Mongolian pine forest. 26 fungal species identified from three tree samples. Each tree sample harbored a fungal endophyte community with a unique structure. The invasion of woodwasp appear to be promoted by the fungal community in the Mongolian pine woodlands. Pathogenic fungi richness was four times higher in infested and unhealthy uninfested compared to healthy uninfested trees. Sphaeropsis sapinea was the most dominant pathogenic fungus in Mongolian pine forest, and infested healthy Mongolian pine without wounding, but a with lower incidence of without wounding (38.72%) than wound ones (83.22%). Collectively, these data indicated that the fungal disease may have caused the initial reason of the decline of the Mongolian pine forest, and also provided convenient conditions for the successful colonization of woodwasp. The woodwasp attacked stressed Mongolian pine trees and accelerated its decline.