Toxoplasma gondii is an intracellular parasitic protozoan that poses a significant risk to pregnant women and immunocompromised individuals. T. gondii tachyzoites duplicate rapidly in host cells during acute infection through endodyogeny. This highly regulated division process is accompanied by complex gene regulation networks. TgAP2XII-9 is a cyclical transcription factor, but its specific role in the parasite cell cycle is not fully understood. Here, we demonstrate that TgAP2XII-9 is identified as a nuclear transcription factor and is dominantly expressed during the S/M phase of the tachyzoite cell cycle. CUT&Tag results indicate that TgAP2XII-9 targets key genes for the moving junction machinery (RON2, 4, 8) and daughter cell inner membrane complex (IMC). TgAP2XII-9 deficiency resulted in a significant downregulation of rhoptry proteins and rhoptry neck proteins, leading to a severe defect in the invasion and egress efficiency of tachyzoites. Additionally, the loss of TgAP2XII-9 correlated with a substantial downregulation of multiple IMC and apicoplast proteins, leading to disorders of daughter bud formation and apicoplast inheritance, and further contributing to the inability of cell division and intracellular proliferation. Our study reveals that TgAP2XII-9 acts as a critical S/M-phase regulator that orchestrates the endodyogeny and apicoplast division in T. gondii tachyzoite. This study contributes to a broader understanding of the complexity of the parasite’s cell cycle and its key regulators. Overall design: To assess the functions of TgAP2XII-9 in T. gondii, an indole-3-acetic acid (IAA) degradation (mAID) system was used to generate an inducible knockdown (iKD) of TgAP2XII-9 parasites (iKD TgAP2XII-9). Potentially regulated genes of the transcription factor TgAP2XII-9 were investigated by RNA-seq using TgAP2XII-9 iKD parasites with or without IAA treatment for 24 hours. Three biological replicates were employed. And the raw data was already posted on SRA database under project PRJNA1070975. To further characterize the direct target genes of TgAP2XII-9, CUT&Tag experiments were performed using the endogenously 3xHA tagged parasite and RH strain.