Accurately estimating the state-of-health (SOH) of lithium-ion batteries is crucial for efficient, reliable, and safe use. However, the degradation of these batteries involves complex and intricate failure mechanisms that cannot be fully captured by a single model. To tackle this challenge, we propose an SOH estimation method based on Bayesian Model Averaging (BMA), which effectively accounts for both parameter and model uncertainties by combining estimations from different model implementations. It provides both point-value estimates and the probability distribution estimates, delivering results in a fraction of a second. Evaluated on three open-source datasets, the maximum absolute error of SOH estimation is within 0.03, and the Continuous Ranked Probability Score is within 0.015. Compared to optimal individual models, the proposed BMA method reduces the prediction error of point estimates by half to two-thirds. Additionally, the prediction error for probability estimation decreases by an order of magnitude. Moreover, the comparison studies with respect to the Gaussian Process Regression model and the Quantile Regression Forests model demonstrate the applicability and superiority of proposed method. These results highlight the potential of the BMA method to advance battery SOH estimation and facilitate reliable battery management.