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We consider a Bayesian multi‐model fault slip estimation (BMMFSE), which incorporates many candidates of the underground structure (Earth structure and plate boundary geometry) model characterized by a prior probability density function (PDF). The technique is used to study long‐term slow slip events (L‐SSEs) that occurred beneath the Bungo Channel, southwest Japan, in around 2010 and 2018. We here focus on the two advantages of BMMFSE: First, it allows for estimating slip distribution without introducing relatively strong prior information such as smoothing constraints, by combining a fully Bayesian inference and better consideration of model uncertainty to avoid overfitting. Second, the posterior PDF for the underground structure is also obtained during the fault slip estimation, which can be used as priors for the estimation of slip distribution for recurring events. The estimated slip distribution obtained using BMMFSE agreed better with the distribution of deep tectonic tremors at the down‐dip side of the main rupture area than those based on stronger prior constraints when the corresponding Coulomb failure stress changes are compared. This finding suggests a mechanical relationship between the L‐SSE and the synchronized tremors. The use of the posterior PDF of the underground structure estimated for the 2010 L‐SSE as prior PDF for the 2018 event resulted in more consistent estimation with the data, indicated by a smaller value of an information criterion. Plain Language Summary: This study attempts to accurately estimate the slow motion between two plates, which does not produce seismic waves and is known as slow slip events (SSEs), targeting those occurred in southwest Japan. This was accomplished by analyzing satellite data of ground movement during the SSEs using a novel approach called the Bayesian multi‐model fault slip estimation (BMMFSE) framework, which considers multiple candidates of assumptions for Earth structures. BMMFSE stabilizes the analysis and removes artifacts from the estimation results which are otherwise introduced because of the choice of a wrong Earth model. These advantages were validated by comparing the estimation results obtained based on previous approaches that do not consider multiple Earth models. The result of BMMFSE exhibited spatial distributions of motion between plates that are more consistent with other slow earthquakes which occurred synchronously in the nearby fault. In addition, BMMFSE improved the consistency of the estimates with the data by taking over the model uncertainty in the sequential analysis of repeated SSEs. Key Points: Fault slip distributions for slow slip events (SSE) at southwest Japan were estimated considering the uncertainty of underground structureThe mechanical relationship between the SSEs and synchronized tectonic tremors are better justified than in previous studiesInformation criterion indicates that estimates for recurring SSEs taking over model uncertainty result in better consistency with the data [ABSTRACT FROM AUTHOR]