In this paper, we design a segment training based individual channel estimation (STICE) scheme for the classical two-way relay network (TWRN) with multi-pair sources (MPS) and amplify-and-forward (AF). We adopt the linear minimum mean square error (LMMSE) channel estimator to minimize the mean square error (MSE) without channel estimation error, where the optimal power allocation strategy from the relay for different sources is obtained. Then the MSE gains are given with different source pairs among the proposed power allocation scheme and the existing power allocation schemes. Numerical results show that the proposed method outperforms the existing ones.