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Description: Due to complex three-dimensional (3D) heterogeneous structures, conventional one-dimensional (1D) analysis techniques using onshore seismograms can yield incorrect estimation of earthquake source parameters, especially dip angles and centroid depths of offshore earthquakes. Combining long-term onshore seismic observations and numerical simulations of seismic wave propagation in a 3D model, we conducted centroid moment tensor (CMT) inversions of earthquakes along the Nankai Trough between April 2004 and August 2019 to evaluate decade-scale seismicity. Green’s functions for CMT inversions of earthquakes with moment magnitudes of 4.3–6.5 were evaluated using finite-difference method simulations of seismic wave propagation in the regional 3D velocity structure model. Our CMT solutions were generally better than those in the catalogue based on regional 1D analysis, especially for offshore earthquakes. By introducing the 3D structures of the low-velocity accretionary prism and the Philippine Sea Plate, dip angles and centroid depths for offshore earthquakes were well-constrained. Our 3D CMT catalogue and published slow earthquake catalogues depicted spatial distributions of slip behaviours on the plate boundary along the Nankai Trough. The regular and slow interplate earthquakes were separately distributed, with these distributions reflecting the heterogeneous distribution of effective strengths along the Nankai Trough plate boundary. By comparing the spatial distribution of seismic slip on the plate boundary with the slip-deficit rate distribution, regions with strong coupling were clearly identified. Preprint has been available in EathArXiv. The CMT catalogue has been also available https://doi.org/10.5281/zenodo.3523582