Remediating heavy metal (HM)-contaminated farmlands and sequestering soil carbon for emission reduction have been prominent topics in environmental research in recent years. However, few studies have looked into the soil greenhouse gas (GHG) impacts of growing hyperaccumulators in composite HM-contaminated farmland, as well as agronomic measures to remediate soil HMs while mitigating GHG emissions. To investigate fertilization measures to improve phytoremediation efficiency and mitigate GHG emissions, S. photeinocarpum was planted with three different fertilization measures on farmland contaminated by lead-zinc (Pb-Zn) mines (1200 kg ha−1 eggshell, 125 kg ha−1 28-homobrassinolide, and 16.7 kg ha−1 mineral potassium fulvic acid) during its growth period. The findings are as follows: Eggshell application significantly enhanced the translocation factor (TF) of Pb, Zn, and cadmium (Cd) from the roots to the shoots of Solanum photeinocarpum. Moreover, eggshells notably increased the bioaccumulation factor (BCF) of Cd and Pb in plant shoots by 120.75% and 159.09%, respectively. Regarding GHG emissions, the combined application of eggshells and 28-homobrassinolide substantially lowered the global warming potential (GWP) of the soil. Correlation analyses revealed that eggshell application increased the relative abundance of the Gemmatimonadota bacterial phylum in the soil, facilitating Pb and Cd migration from the roots to shoot tissues in S. photeinocarpum. Eggshell use inhibited nitrate nitrogen (NO3−-N) transformation into nitrous oxide (N2O) by the Myxococcota bacterial phylum and reduced N2O release from the soil. The application of low-cost eggshells can achieve a win-win situation of soil HM remediation and GHG emission reduction, as well as provide simple and scalable management measures for HM-contaminated farmland.