MIMO two-way relay is a well known method for realizing highly efficient multi-hop relay networks. Previous works in MIMO two-way relay network have focused on an equidistant topology of the relay nodes. However such a topology rarely exists in a practical situation. In a non-equidistant topology, the end-to-end network capacity degrades severely due to the bottleneck link caused by uneven SNR. Furthermore, the end-to-end network capacity also degrades at high SNR due to overreach interference from far nodes existing in multi-hop relay networks. In this paper, we focus on the non-equidistant topology of the MIMO two-way relay network, and apply three transmit power allocation schemes for balancing and maximizing the SINR of each link, i.e. Eigen-value based Power Allocation (EPA), Optimal Power Allocation (OPA) and Distributed Power Allocation (DPA) schemes. The efficiency of proposed schemes is validated using numerical simulations.