Abstract: In the long-term prediction of battery degradation, the data-driven method has great potential with historical data recorded by the battery management system. This paper proposes an enhanced data-driven model for Lithium-ion (Li-ion) battery state of health (SOH) estimation with a superior modeling procedure and optimized features. The Gaussian process regression (GPR) method is adopted to establish the data-driven estimator, which enables Li-ion battery SOH estimation with the uncertainty level. A novel kernel function, with the prior knowledge of Li-ion battery degradation, is then introduced to improve the modeling capability of the GPR. As for the features, a two-stage processing structure is proposed to find a suitable partial charging voltage profile with high efficiency. In the first stage, an optimal partial charging voltage is selected by the grid search; while in the second stage, the principal component analysis is conducted to increase both estimation accuracy and computing efficiency. Advantages of the proposed method are validated on two datasets from different Li-ion batteries: Compared with other methods, the proposed method can achieve the same accuracy level in the Oxford dataset; while in Maryland dataset, the mean absolute error, the root-mean-squared error, and the maximum error are at least improved by 16.36%, 32.43%, and 45.46%, respectively.