The estimation of the state of health (SOH) of lithium-ion batteries is of great importance to ensure the safe and stable operation of a lithium-ion battery management system (BMS). Accurate estimation of SOH can effectively prevent unnecessary losses of lithium-ion batteries due to failures. Therefore, a Bayesian-optimized Gaussian process regression (BO-GPR) method is proposed for SOH estimation. Firstly, the ageing characteristics reflecting the SOH of the battery are extracted from the charge/discharge time and incremental capacity (IC) curve, and the correlation between the health characteristics and the SOH is analysed by means of grey correlation (GRA). On the other hand, a Bayesian optimization algorithm is used to automatically find the optimal hyperparameters of the GPR model and trained using the battery dataset to obtain the SOH estimating model. To validate the effectiveness of the method, the datasets provided by NASA and Oxford are used as experimental objects and compared with different data-driven models to verify the accuracy and reliability of the proposed model. The experimental results show that the method proposed in this paper has a high accuracy in the estimation of the SOH, with the maximum average estimation error being within 1%.