Fungal endophytes are fungi that live for a significant part of their life cycle internally and asymptomatically (without causing any apparent tissue damage) in plants. For grasses, these endophytes are often specialized, systemic, and vertically transmitted. Pangquangou Nature Reserve is located in the middle of the of Luliang Mountain range. It was established for the conservation of the first-grade State protection animal, Crossoptilon mantchuricum, and the cold-temperate coniferous forest. It plays a significant role in water conservation, eco-tourism, biodiversity maintenance, and other functions in Pangquangou Nature Reserve. Many studies have been conducted; however few of them have examined the distribution and mechanism of fungal endophytes associated with common plants in Pangquangou Nature Reserve. In the present study, we assessed the endophyte infection rate of dominant plants in four different forest communities. Our objective was to investigate the effects of endophyte fungi association on soil properties, soil enzyme activity, and soil microbial communities in native habitats. We surveyed endophyte infection rates of four common plants (Festuca rubra, Avena fatua, Carex alexeenkoana, and Poa annua). We also analyzed the soil total carbon (C), total nitrogen (N), and total sulfur (S) with an Elemental Analyzer, and soil microbial community composition were assayed by using the high-throughput sequencing technique. Our results showed that soil water content and ratio of carbon and nitrogen were the main factors affecting the endophyte infection rates of Festuca rubra and Carex alexeenkoana, and the soil C, N, S and soil water content were positively correlated with the endophyte infection rate of Festuca rubra. There were strong positive correlations between soil invertase and endophyte infection rates of Festuca rubra, as well as urease and acid phosphatase. However, Carex alexeenkoana exhibited opposite results to those of Festuca rubra. Inocybaceae is the dominant fungi of soil microbial community in Larix principis-rupprechtii community, but had different bacterial compositions in soil microbial community under four forest communities. Overall, there were different correlations between fungal endophyte infection rate and soil properties under different communities, and the effects of ecological factors were also different. Endophyte fungal contributed to change soil microbial community structure, and led to varying soil fungi and bacteria compositions in different forest communities. Our findings can help with further understanding the distribution of fungal endophytes associated with common plants in native habitats and the influence of endophyte infected plants on soil microbial community structure and ecological functions in ecosystems.