As the first transcriptional milestone in life, zygotic genome activation (ZGA) driven by pioneer factors is a hallmark of totipotency, enabling embryos to transition from maternal to zygotic control. Yet, the mechanisms governing the totipotent state of embryonic chromatin remain a central unresolved question in developmental biology. Here we identified IntS11, a Pol II-associated protein, as a critical totipotency factor in Drosophila. We demonstrate that maternal IntS11 controls totipotent state of chromatin, ensuring proper ZGA by coordinating the transcription machinery assembly. Specifically, IntS11 mediates de novo Pol II recruitment and directs pioneer factors Zelda and GAF to zygotic gene regulatory regions. Our findings unveil a fundamental principle linking IntS11, pioneer factor binding, and Pol II engagement, providing novel insights into orchestration of ZGA.