Optical　Coherence　Tomography　(OCT)　was　successfully　applied　in　the　microstructure　imaging　of　biological　tissue　after　being　proposed　firstly　in　1991　by　the　researchers　of　MIT.　As　a　novel　optical　imaging　technology,　it　mainly　uses　interference　principles　to　achieve　noninvasive　and　high　resolution　visualization　of　samples.　OCT　works　analogously　to　an　ultrasound　scanner,　the　major　difference　is　that　ultrasound　pulses　are　replaced　by　broadband　light.　According　to　whether　need　for　mechanical　axial　scan　in　the　depth　direction,　it　can　be　classified　into　the　time-domain　OCT　(TD-OCT)　and　frequency-domain　OCT　(FD-OCT).　The　FD-OCT　system　overmatches　the　TD-OCT　in　imaging　speed　because　of　its　depth　collection　advantage.　But　in　the　reconstructive　image　of　FD-OCT　detection,　the　complex-conjugate　ambiguity　will　seriously　deteriorate　the　imaging　effect　of　tomogram.　So　the　technique　of　removing　the　complex-conjugate　image　is　employed　that　is　called　complex　FD-OCT.　The　complex　FD-OCT　has　widely　application　in　many　fields,　especially　in　the　refractive　index　measurement.　The　refractive　index　is　an　important　parameter　characterizing　light　propagation　in　the　medium.　In　the　paper,　we　present　a　method　to　measure　the　average　refractive　index　of　the　sample　with　substrate　calibration　by　using　complex　FD-OCT　method,　in　which　we　can　calculate　it　without　depending　on　the　parameters　of　system　such　as　spectral　width　of　light　source.　Due　to　the　measurement　of　average　refractive　index　relative　to　the　actual　thickness　and　optical　length,　it　is　necessary　to　obtain　them　of　the　sample　experimentally.　The　complex　FD-OCT　method　can　easily　achieved　the　optical　length　via　measuring　the　positions　of　the　sample＇s　front　and　rear　surfaces.　In　the　experiment,　the　coverslip　(the　borosilicate　glass)　is　chosen　as　the　sample　and　the　calibration　substrate.　We　make　use　of　the　substrate　to　load　the　sample　on　it,　and　then　the　tomogram　of　the　sample　can　be　achieved　by　means　of　OCT＇s　lateral　scan　in　the　edge　of　the　sample　and　complex　FD-OCT　method.　According　to　the　experimental　results,　we　can　acquire　the　sample＇s　tomographic　information　and　position　of　the　substrate.　The　ratio　of　actual　thickness　and　optical　length　can　be　indirectly　calculated　out　with　the　pixel　number　obtained　by　analyzing　the　image　data.　So　with　only　one　time　scan,　we　can　complete　the　measurement　of　average　refractive　index　of　the　sample　without　aid　of　other　instruments.