Macrophages are essential for the proliferation and spread of Toxoplasma gondii. Modulating macrophage activation to improve the inflammatory environment is an effective approach for disease treatment. However, the molecular mechanism through which T. gondii alters macrophage function remain unknown. Based on transcriptomic data analysis of various macrophage types infected with T. gondii, current research revealed differences in the regulation of macrophage functions among strains with different virulence: RH was primarily involved in cell cycle regulation, ME49 was associated with cAMP signaling, and CEP mainly participated in ion channel activity. All three T. gondii strains were involved in regulating immune response activation, including leukocyte adhesion and the MAPK signaling pathway. Nineteen shared DEGs associated with macrophage phagocytosis or polarization were identified through the GeneCards database, and PPI analysis confirmed Il6 as the hub gene in the regulatory network. In vivo and in vitro experiments showed that the YZ-1 strain significantly regulated the expressions of eight DEGs (Il6, Rel, Cd83, Myc, Adora2b, Egr2, Gja1 and Nr4a2), and promoted macrophage phagocytic activity and induced M1 polarization, confirming a significant correlation with Il6. This study revealed the dissimilarities and commonalities in macrophage function regulated by T. gondii strains of different virulence, and identified key molecules involved in the regulation of macrophage phagocytosis and polarization during T. gondii infection. This is crucial for identifying potential drug targets against T. gondii and provides a new perspective on the etiopathogenesis and therapeutic approaches for toxoplasmosis.