A sum frequency generation (SFG) vibrational micro-spectroscopy system was developed to examine buried heterogeneous biointerfaces. A compact optical microscope was constructed with total-internal reflection (TIR) SFG geometry to monitor the tightly focused SFG laser spots on interfaces, providing the capability of selectively probing different regions on heterogeneous biointerfaces. The TIR configuration ensures and enhances the SFG signal generated only from the sample/substrate interfacial area. As an example for possible applications in biointerfaces studies, the system was used to probe and compare buried interfacial structures of different biological samples attached to underwater surfaces. We studied the interface of a single mouse oocyte on a silica prism to demonstrate the feasibility of tracing and studying a single live cell and substrate interface using SFG. We also examined the interface between a marine mussel adhesive plaque and a CaF2 substrate, showing the removal of interface-bonded water molecules. This work also paves the way for future integration of other microscopic techniques such as TIR-fluorescence microscopy or nonlinear optical imaging with SFG spectroscopy for multimodal surface or interface studies.