Interseismic strain around southwest Japan can be attributed to slip phenomena on the plate interface and processes inside the continental plate, such as block motions and inland fault slips. Although many crustal deformation analyses have been carried out, the simultaneous estimation of these phenomena and comprehensive discussion regarding the effect on the total strain budget remain topics to be investigated. In this study, we conducted numerical experiment to evaluate the possibility of simultaneously monitoring the spatiotemporal evolution of interseismic fault slips and block motions based on state-space modeling. We aimed to estimate fault slips and block motions using the time series of dense continuous Global Navigation Satellite System sites covering southwest Japan, encompassing 25 years from 1996 onward. We calculated synthetic block motions of the forearc region, monotonically increasing back slips on block boundary faults, and long-term slow slip events in the Tokai region, Kii Channel, and Bungo Channel. Subsequently, we generated the expected synthetic displacement time-series at GNSS stations. Applying Kalman filtering, we successfully estimated the spatiotemporal evolution of block motions, cumulative back slips, multiple slow slip events occurring in different regions. Although the contributions of fault slips and block motions showed slight trade-off, main characteristics of the slip distributions and the direction of block motions were well-recovered. We recovered slow slip events with slips of 5–10 cm or larger. We investigated the estimation uncertainty and separation precision of the unknown parameters using the covariance matrix estimated by Kalman filtering. Focusing on the structure of the non-diagonal component of the covariance matrix, we evaluated the complex effects of site and subfault locations on the estimated slip spatial distribution bias. For instance, the extent of the correlation between subfaults suggested that the three slow slip regions have different tendency of the uncertainties of slip areas, extending toward landside, seaward, or both of them. Our framework enables the comprehensive evaluation of the contributions and uncertainties of various deformation sources covering the entire subduction zone.Graphical abstract