The power quality estimation for distribution network connected DG (distributed generation) is important in the power system. The significance testing for power quality indicator is less used in traditional power quality evaluation. However, the power quality indicator is affected by various factors of the power system, which seriously impact the power quality evaluation result. To solve this problem, A novel power quality comprehensive estimation model based on multi-factor variance analysis for distribution network with DG is proposed in this paper, in which the significance testing is carried out for power quality indicator with the various system factors, and then to generate the evaluation weights in different levels, further to obtain the power quality assessment results for single node. And then, the dual-significance tests are carried out to generate the weight of node and to obtain the comprehensive estimation result of whole system. At last, an example is developed to validate that, compared with the traditional power quality evaluation, the proposed method is more reasonable and effective in the power quality evaluation for DG connected distribution network.