Deep Neural Networks (DNNs) are known to be vulnerable to backdoor attacks, posing concerning threats to their reliable deployment. Recent research reveals that backdoors can be erased from infected DNNs by pruning a specific group of neurons, while how to effectively identify and remove these backdoor-associated neurons remains an open challenge. Most of the existing defense methods rely on defined rules and focus on neuron's local properties, ignoring the exploration and optimization of pruning policies. To address this gap, we propose an Optimized Neuron Pruning (ONP) method combined with Graph Neural Network (GNN) and Reinforcement Learning (RL) to repair backdoor models. Specifically, ONP first models the target DNN as graphs based on neuron connectivity, and then uses GNN-based RL agents to learn graph embeddings and find a suitable pruning policy. To the best of our knowledge, this is the first attempt to employ GNN and RL for optimizing pruning policies in the field of backdoor defense. Experiments show, with a small amount of clean data, ONP can effectively prune the backdoor neurons implanted by a set of backdoor attacks at the cost of negligible performance degradation, achieving a new state-of-the-art performance for backdoor mitigation.