We study the effects of the degree distribution in mutual synchronization of two-layer neural networks. We carry out three coupling strategies: large-large coupling, random coupling, and small-small coupling. By computer simulations and analytical methods, we find that couplings between nodes with large degree play an important role in the synchronization. For large-large coupling, less couplings are needed for inducing synchronization for both random and scale-free networks. For random coupling, cutting couplings between nodes with large degree is very efficient for preventing neural systems from synchronization, especially when subnetworks are scale-free.