Eupatorium adenophorum , a most harmful invasive plant in China, contains toxicants to microbes. It is beneficial to economical and effective elimination this plant by the harmless treatment and resource utilization. In this paper, the qualities of E. adenophorum bio-compost and natural compost were measured, thenE. adenophorum bio-compost (M), chemical fertilizer (CF) and bio-compost+chemical fertilizer (CFM) were added into soil to study their influences on soil organic matter, nutrients and microbes by incubation method in order to get information on the evaluation of M quality, microbial toxicity and fertilizer efficiency. The results showed that M was conformed to NY525-2011 (the National Standard of Organic Fertilizer) except moisture higher than that of Standard. M quality was better than natural compost. During 120 day incubation, CF decreased the quantities of fungi and actinomycetes in contrast to bacteria which changed little. Providing soil with CFM or M increased organic matter, microbial carbon and nitrogen, and the quantities of bacteria, fungi and actinomycetes in soils. In the soil with CF, alkaline-hydrolyzed N and the activities of soil urease and sucrase in early incubation stage were much higher than CK (blank control), but became similar to CK in the late stage. In the soil with CFM or M, alkaline-hydrolyzed N was higher than CK and changed gently in whole incubation period, the activities of soil catalase, urease, acid phosphatase and sucrose were higher than CF and CK. Therefore, the influence of M on soil organic matter, nutrients, and microbial biomass and soil enzyme activity was similar to common organic fertilizers.