To investigate the effects of dazomet fumigation and different application times of bioorganic fertilizer on soil physicochemical and biological properties as well as the incidence of watermelon Fusarium wilt disease, five treatments, i.e. un-treated control (CK), dazomet fumigation, applying different times of bioorganic fertilizer into dazomet fumigated soil during the watermelon cultivation, were conducted in a greenhouse with severely Fusarium wilt. The results showed that the application of bioorganic fertilizer in dazomet fumigated soil did not decrease the population of F. oxysporum and the disease incidence, but significantly increased the bacterial and fungal numbers and altered the microbial community structure. In addition, the application of bioorganic fertilizer decreased soil pH, and excessive application would lead to the accumulations of nitrate and salinity. To improve soil microbial community and prevent soil salinization, the optimal application of bioorganic fertilizer was applying one time when transplantation and 1-2 times during the cultivation.