We investigate a scheduling scheme incorporating network coding and channel varying information for the two-way relay networks. Our scheduler aims at minimizing the time span needed to send all the data of each source of the network. We consider three channel models, time invariant channels, time varying channels with finite states and time varying Rayleigh fading channels. We formulate the problem into a manageable optimization problem, and get a closed form scheduler under time invariant channels and time varying channel with finite channel states. For Rayleigh fading channels, we focus on the relay node operation and propose heuristic power allocation algorithm resemblant to water filling algorithm. By simulations, we find that even if the channel fluctuates randomly, the average time span is minimized when the relay node transmits/schedules network coded data as much as possible.