A novel adaptive cross-layer optimal power allocation (OPA) scheme over physical layer and data-link layer for two-way relaying system with amplify-and-forward policy (TWR-AF) is proposed in this paper. Our goal is to find the optimal power allocation factors under each channel state information (CSI) to maximize the sum throughput of two sources under total transmit power constraint in the physical layer while guaranteeing the statistical delay quality-of-service (QoS) requirement in the data-link layer. By integrating information theory with the concept of effective capacity, the OPA problem is formulated into an optimization problem to maximize the sum effective capacity. It is solved through Lagrange multiplier approach, and the optimal power allocation factors are presented. Simulations are developed and the results show that the proposed cross-layer OPA scheme can achieve the best sum effective capacity with relatively low complexity when compared with other schemes. In addition, the proposed cross-layer OPA scheme achieves the maximal sum effective capacity when the relay is located in (or near) the middle of the two source nodes, and the sum effective capacity becomes smaller when the difference between two QoS exponents becomes larger.