We propose a Fourier modal method (FMM) based through-focus scanning optical microscopy (TSOM) featuring sub-nano scale measurement tolerance. TSOM is very recently conceptualized non-destructive optical metrology technique just at the beginning stage of research. Nowadays the reliability and feasibility of TSOM concept is subject to controversy. We experimentally demonstrate stable nano-scale metrology of the FMM-based TSOM for the verification of the TSOM metrology and provide a numerical tool for true nano-meter scale TSOM through devising the FMM based TSOM scheme. By considering the illumination light parameters of incidence angle, polarization, degree of coherence, illumination numerical aperture, and collection numerical apertures in the FMM modeling of TSOM image acquisition, we reach precise agreement between the calculated and experimentally measured TSOM images. The essential elements of the FMM based TSOM for achieving high-level consistency are elucidated.