To improve the performance of a relay system with multiple channels, the following issues should be addressed. Namely, how to allocate the power at source and relay to subchannels, how to pair subchannels of the first and second hops, and which users should be scheduled to which subchannel pair. Considering these issues in the design of an optimal joint resource allocation scheme in orthogonal channels, in this paper we study a multi-user network with single regenerative relay node. A stochastic optimization problem to maximize system ergodic throughput with joint transmission power constraint and user average data rate is formulated. To satisfy user average data rate request, a scheme with a weighted factor associated to each user at each time slot is proposed. The stochastic approximation method is utilized to estimate this weighted factor and the proof of optimality is given. With the help of this weighted factor, the problem is converted into a deterministic optimization problem in each time slot and the Lagrange dual method can be employed to derive the optimal solution. Finally, the Stochastic Optimal Programming (SOP) is used to evaluate the performance by computer simulations.