Abstract: The paper aims to study the changes of microorganism and harmful biology in the process of organic fertilizer oxygen fermentation. The author used the plate dilution method and established a mathematical model, in order to provide a theoretical basis to determine the production technology and fermentation time for organic fertilizer fermentation under natural conditions of windrow type. The results showed that the number of fungi and mildew presented a three quadratic polynomial equation curve with the fermentation time, and decreased with the prolonging of the fermentation time. The number of bacteria presented a‘down-up-down’ three quadratic polynomial equation curve with the prolonging of the fermentation time. Escherichia coli value presented a three quadratic polynomial equation curve with the fermentation time, and increased with the prolonging of the fermentation time. Mortality of ascarid eggs presented a two quadratic polynomial equation curve with the fermentation time, and increased with the prolonging of the fermentation time, and reached the maximum around 110 days. Under natural conditions, fermentation time of windrow type organic fertilizer should be within 100-120 days.