Heterogeneous Networks (HetNets), where Low Power Nodes (LPN) are deployed under the coverage of Macro Base Stations (MBS), are promising to boost the spectrum efficiency per unit area. However, this hierarchical architecture also brings new problems, like severe inter-cell interference. The randomly deployed LPNs, and the co-existence of the cross-tier and intra-tier interference make it challenging to design the effective frequency reuse schemes, which can have significant influences on the user experience and the network capacity. In this paper, we explore the frequency reuse problem in HetNets for interference mitigation. Firstly, Partial Spectrum Reuse (PSR) scheme is adopted to mitigate the cross-tier interference, where MBSs can use all available spectrums while LPNs can only use part of the channels based on their traffic load. Then, the channel allocation scheme is further optimized to mitigate the intra-tier interference. As the channel allocation problem is NP-hard, we propose a greedy channel allocation scheme based on a weighted conflict graph, where cross-tier and intra-tier interference are both considered. In addition, our method is practical for channel allocation in real systems. Simulation results show the SINR of cell edge users and the ergodic SINR can be both improved by 3dB as much with our greedy method compared with the random channel allocation scheme.