The　most　recently　proposed　three-dimensional　(3D)　contact　potential-based　discontinuous　deformation　analysis　(3D-CPDDA)　method　is　further　applied　for　wave　propagation　problems　in　rock　masses.　A　viscous　non-reflecting　boundary　is　incorporated　into　the　3D-CPDDA　method　to　minimize　the　wave　reflections.　Furthermore,　a　force　input　method　is　incorporated　to　eliminate　the　contamination　of　scattered　waves　in　the　numerical　solution　and　to　accurately　input　the　incident　wave.　Several　benchmark　problems　about　P-wave/S-wave　propagation　in　homogeneous　rock　masses　and　jointed　rock　masses　are　solved　to　validate　the　modified　3D-CPDDA　method.　The　numerical　results　assessed　by　the　modified　3D-CPDDA　method　agree　well　with　those　obtained　from　analytical　methods,　which　means　that　the　modified　3D-CPDDA　method　can　reliably　and　correctly　simulate　wave　propagation　in　rock　masses.　The　modified　3D-CPDDA　method　warrants　further　investigation.