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We apply the spectroscopy-based stellar-color regression (SCR) method to perform an accurate photometric re-calibration of the second data release from the SkyMapper Southern Survey (SMSS DR2). From comparison with a sample of over 200,000 dwarf stars with stellar atmospheric parameters taken from GALAH+ DR3 and with accurate, homogeneous photometry from $Gaia$ DR2, zero-point offsets are detected in the original photometric catalog of SMSS DR2, in particular for the gravity- and metallicity-sensitive $uv$ bands. For $uv$ bands, the zero-point offsets are close to zero at very low extinction, and then steadily increase with $E (B - V)$, reaching as large as 0.174 and 0.134 mag respectively, at $E (B - V) \sim 0.5$ mag. These offsets largely arise from the adopted dust term in the transformations used by SMSS DR2 to construct photometric calibrators from the ATLAS reference catalog. For the $gr$ bands, the zero-point offsets exhibit negligible variations with SFD $E(B - V )$, due to their tiny coefficients on the dust term in the transformation. Our study also reveals small, but significant, spatial variations of the zero-point offsets in all $uvgr$ bands. External checks using Strömgren photometry, WD loci and the SDSS Stripe 82 standard-star catalog independently confirm the zero-points found by our revised SCR method.