Abstract We employ the corrected Gaia Early Data Release 3 photometric data and spectroscopic data from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) DR7 to assemble a sample of approximately 0.25 million FGK dwarf photometric standard stars for the 12 J-PLUS filters using the stellar color regression (SCR) method. We then independently validate the J-PLUS DR3 photometry and uncover significant systematic errors: up to 15 mmag in the results from the stellar locus method and up to 10 mmag primarily caused by magnitude-, color-, and extinction-dependent errors of the Gaia XP spectra as revealed by the Gaia BP/RP (XP) synthetic photometry (XPSP) method. We have also further developed the XPSP method using the corrected Gaia XP spectra by B. Huang et al. and applied it to the J-PLUS DR3 photometry. This resulted in an agreement of 1–5 mmag with the SCR method and a twofold improvement in the J-PLUS zero-point precision. Finally, the zero-point calibration for around 91% of the tiles within the LAMOST observation footprint is determined through the SCR method, with the remaining approximately 9% of the tiles outside this footprint relying on the improved XPSP method. The recalibrated J-PLUS DR3 photometric data establish a solid data foundation for conducting research that depends on high-precision photometric calibration.