The two-stage hydrocracking process has the VGO and/or other heavy fraction oil as the material oil hydrocracked under certain condition to obtain high quality clean product. The catalyst in the first stage of pre-treatment includes at least one kind of bulk phase catalyst comprising complex oxide NixWyOz and oxide MoO3 in the weight ratio 0.1-10 and accounting for 40-100 wt% of total catalyst. The present invention facilitates the hydrocracking operation, increases the treating capacity of the apparatus, increases the service life of the catalyst and raises the quality of the product.