Few researches on high efficiency modified phosphogypsum (MPG) and its resource utilization in bulding materials. This article investigated the effects of different lower temperatures and drying times on the thermodynamic modification mechanism of macroscopic performance and microscopic structure of MPG, and investigates its application in phosphogypsum-based self-leveling mortars (PBSLM). Then, the coupling mechanism of characteristic heavy metals in the modification process (original-modification-hydration) was discussed, and the safety evaluation was conducted on the content of heavy metal elements in the sample. Data from microscopic analysis showed that with the increase of temperature and drying time, the strength of MPG blocks and the decomposition rate of dihydrate gypsum crystal both increased, while the particle size decreased. The degree of crystal decomposition becomes more complete as the temperature rises if the holding time remains constant. As well as, the MPG at 180 °C/7 h, 195 °C/7 h/10 h met the Chinese standard of “Calcined gypsum” (GB/T9776). The heavy metal elements in MPG decreased obviously, caused by the substitution solid solution formed by Ca2+ and Fe3+ and heavy metal ions and the adsorption of calcium sulfate hemihydrate crystals. After hydration of MPG, As and Cd increased slightly because dicalcium phosphate was insoluble in water and soluble in acid, and iron oxide reduced and dissolved Cd. Then, the ecological hazards of heavy metals in hydrated MPG after hydration were evaluated. The results showed that there was no environmental safety problem in the hydrated MPG, but the As and Cr elements in it had an acceptable carcinogenic risk through oral intake. Based on ensuring the safety of MPG, MPG powder was used in PBSLM. The research demonstrates that the basic mechanical properties of the PBSLM produced, when the MPG powder content is 330 g, and cement is 40 g are the best. The heavy metal aqueous solution's leaching amount is lower than China's national standard limit value. (30min fluidity, 24 h-flexural and compressive strength were 154 mm, 5.7 MPa and 10.6 MPa). Finally, based on this research, a set of general evaluation system for safe utilization of solid waste was established according to national standards. This provides theoretical support for the research of heavy metal in PG at low temperature and the ways of harmless and resource utilization.