The network pruning algorithm based on evolutionary multi-objective (EMO) can balance the pruning rate and performance of the network. However, its population-based nature often suffers from the complex pruning optimization space and the highly resource-consuming pruning structure verification process, which limits its application. To this end, this paper proposes an EMO joint pruning with multiple sub-networks (EMO-PMS) to reduce space complexity and resource consumption. First, a divide-and-conquer EMO network pruning framework is proposed, which decomposes the complex EMO pruning task on the whole network into easier sub-tasks on multiple sub-networks. On the one hand, this decomposition reduces the pruning optimization space and decreases the optimization difficulty; on the other hand, the smaller network structure converges faster, so the computational resource consumption of the proposed algorithm is lower. Secondly, a sub-network training method based on cross-network constraints is designed so that the sub-network can process the features generated by the previous one through feature constraints. This method allows sub-networks optimized independently to collaborate better and improves the overall performance of the pruned network. Finally, a multiple sub-networks joint pruning method based on EMO is proposed. For one thing, it can accurately measure the feature processing capability of the sub-networks with the pre-trained feature selector. For another, it can combine multi-objective pruning results on multiple sub-networks through global performance impairment ranking to design a joint pruning scheme. The proposed algorithm is validated on three datasets with different challenging. Compared with fifteen advanced pruning algorithms, the experiment results exhibit the effectiveness and efficiency of the proposed algorithm.