Provided is a method and system with deep learning model generation. The method includes identifying a plurality of connections in a neural network that is pre-associated with a deep learning model, generating a plurality of pruned neural networks by pruning different sets of one or more of the plurality of connections to respectively generate each of the plurality of pruned neural networks, generating a plurality of intermediate deep learning models by generating a respective intermediate deep learning model corresponding to each of the plurality of pruned neural networks, and selecting one of the plurality of intermediate deep learning models, having a determined greatest accuracy among the plurality of intermediate deep learning models, to be an optimized deep learning model.