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Three issues should be taken into account to improve performance in relay system with multiple channels. They are, how to allocate the power at source and relay to the subchannels, how to pair subchannels of the first hop and the second hop, and which users should be scheduled to which subchannel pair. These issues are considered to design the optimal joint resource allocation scheme in multiple orthogonal channels, multiple users system with single regenerative relay node in this paper. The deterministic optimization problem to maximize system throughput with joint transmission power constraint and users' instantaneous data rate request constraint is formulated. Lagrange dual method is employed to derived the optimal solution. Then, the Deterministic Optimal Programming (DOP) is proposed. Finally, the computational complexity of DOP is analyzed and we evaluate the performance of it by computer simulations.