The invention discloses a method for improving the activity of aspergillus niger cellulase by large fragment gene integration, and belongs to the field of gene engineering. According to the method, a large gene segment related to a trichoderma reesei cellulase system is integrated into an aspergillus niger genome once through multiple homologous recombination. The method specifically comprises the following steps of integrating two aspergillus niger genome segments and a hygromycin resistant gene unit box onto a trichoderma reesei genome, afterwards, using the two segments as homologous recombination sites and hygromycin resistance as a screening marker to integrate a large fragment between the two sites on the trichoderma reesei genome onto the aspergillus niger genome. The polyclonal purposes of a cellulase gene and a non-cellulase gene are achieved; therefore, a metabolic network of aspergillus niger is influenced; the activity of the cellulase of the aspergillus niger is improved. The filter paper activity of a strain obtained through the method provided by the invention is 2.17 times the filter paper activity of an original strain.