We demonstrate the utility of optical second harmonic generation (SHG) polarimetry to perform structural characterization of self-assembled zinc-blende/wurtzite III-V nanowire heterostructures. By analyzing four anisotropic SHG polarimetric patterns, we distinguish between wurtzite (WZ), zinc-blende (ZB) and ZB/WZ mixing III-V semiconducting crystal structures in nanowire systems. By neglecting the surface contributions and treating the bulk crystal within the quasi-static approximation, we can well explain the optical SHG polarimetry from the NWs with diameter from 200-600 nm. We show that the optical in-coupling and out-coupling coefficients arising from depolarization field can determine the polarization of the SHG. We also demonstrate micro-photoluminescence of GaAs quantum dots in related ZB and ZB/WZ mixing sections of core-shell NW structure, in agreement with the SHG polarimetry results. The ability to perform in situ SHG-based crystallographic study of semiconducting single and multi-crystalline nanowire heterostructures will be useful in displaying structure-property relationships of nanodevices.