Microscopic　vision　system　with　stereo　light　microscope　(SLM)　has　been　applied　to　surface　profile　measurement.　If　the　vertical　size　of　a　small　object　exceeds　the　range　of　depth,　its　images　will　contain　clear　and　fuzzy　image　regions.　Hence,　in　order　to　obtain　clear　stereo　images,　we　propose　a　microscopic　sequence　image　fusion　method　which　is　suitable　for　SLM　vision　system.　First,　a　solution　to　capture　and　align　image　sequence　is　designed,　which　outputs　an　aligning　stereo　images.　Second,　we　decompose　stereo　image　sequence　by　wavelet　analysis　theory,　and　obtain　a　series　of　high　and　low　frequency　coefficients　with　different　resolutions.　Then　fused　stereo　images　are　output　based　on　the　high　and　low　frequency　coefficient　fusion　rules　proposed　in　this　article.　The　results　show　that　Delta　w(1)(Delta　w(2))　and　Delta　Z　of　stereo　images　in　a　sequence　have　linear　relationship.　Hence,　a　procedure　for　image　alignment　is　necessary　before　image　fusion.　In　contrast　with　other　image　fusion　methods,　our　method　can　output　clear　fused　stereo　images　with　better　performance,　which　is　suitable　for　SLM　vision　system,　and　very　helpful　for　avoiding　image　fuzzy　caused　by　big　vertical　size　of　small　objects.　(C)　2016　Wiley　Periodicals,　Inc.