Lignocellulosic ethanol has been widely concerned because of its green cleaning and renewable advantages. However, the fermentation residues, which major component is lignin, have not been effectively used. Most of them have been burned or dumped into the environment, result in resources wasting, environmental pollution and other problems. In this paper, lignocellulosic ethanol fermentation residue was mixed with conventional chemical fertilizer to synthesize woody residue compound fertilizer in shaking granulator. The effects of the fertilizer on nitrogen and phosphorus availability, urease and soil microbial quantity were studied. After conductivity soil column percolation tesst, soil urease activity test and microbial diversity test, results showed that the fertilizer could reduce urease activity, the release period was prolonged, the volatilization of NH3-N was reduced, the utilization efficiency of fertilizer was improved, the microbial activity and diversity were improved. All of these shown that woody residue compound fertilizer was alleviated the effect of on ecological environment than common fertilizer. It could not only realize the clean utilization of renewable biomass resources, but also adjust the chemical fertilizer application structure in the course of agroforestry application.