All alveolates including apicomplexan parasites contain an inner membrane complex (IMC) underneath the plasma membrane. The IMC is synthesized de novo during asexual replication (including endodyogeny, endopolygeny, and schizogony) and serves as a crucial scaffold for supporting cytoskeletal structures and the glideosome machinery for parasite locomotion. However, the mechanism(s) underlying the membrane biogenesis in the IMC are not well understood. Using a clinically-relevant and globally-prevalent pathogenic protist model, Toxoplasma gondii, we identified the TgVPS13A bridging the IMC to the endoplasmic reticulum (ER) - the major site of phospholipid synthesis. The multi-modular TgVPS13A plays a crucial role in the IMC biogenesis, functioning in concert with an ER-resident VAP protein (TgVAP) and a novel lipid scramblase (TgDAT1). TgDAT1 is recruited for the progeny formation sites during the early stages of budding. Conditional depletion of TgVPS13A, TgDAT1 or TgVAP results in collapse of the inner membrane complex, leading to parasite death, as visualized by endodyogeny-specific organelle markers. GFP-Lact-C2, a biosensor of phosphatidylserine and phosphatidylthreonine lipids made in the ER and enriched in the IMC, also mislocalizes upon protein depletion. In conclusion, we propose that TgVPS13A, together with TgVAP and TgDAT1, bridge the ER and IMC and mediate the inter-organelle transport of lipids, thus contributing to the organelle biogenesis and daughter budding in T. gondii.