Network topology measurement is an important component in network research. Network tomography is able to accurately infer network topology by using end-to-end measurement without cooperation of internal routers. Unfortunately, traditional network tomography methods can not accurately estimate topology in the non-stationary network due to the variability of traffic distribution. In this paper, we present a novel network topology inference method based on subset structure fusion for accurate topology inference in the non-stationary network. First, we propose an end-to-end measurement method named threepacket to accurately probe the three-leaf-nodes subset structures of the network without the assumption that the packet delay or loss follows a stable distribution. Second, we propose a metric for the shared path length based on the structural characteristics of the subset structures to fuse these subset structures into a correct complete topology. The analytical and simulation results show that our method is more applicable for topology inference in the non-stationary network compared with the existing methods. INDEX TERMS End-to-end measurement,network tomography,non-stationary network,subset structure fusion,topology inference.