When there are many suspected loss links, the links in the path with a higher pass rate are assumed to be nondrop packet links or assuming that the link with the largest number of shares is a loss link, but this assumption lacks valid proof. In order to overcome these shortcomings, this paper proposes a link loss inference algorithm with network topology aware. The network model is established based on the historical data of the network operation and network topology characteristics. A weighted relative entropy ranking method is proposed to quantify the suspected packet loss links in each independent subset. The packet loss rate of the packet loss link is obtained by solving the unique solution of the simplified nonsingular matrix. Through simulation experiments, it is verified that the proposed algorithm has achieved better results in terms of congestion link determination and link loss rate estimation accuracy.