Placenta defects are one of the major causes of miscarriages, yet the underlying mechanisms remain poorly understood. We demonstrate that trophoblast-specific depletion of the acetyltransferase Kat5, or introduction of acetylation-defective mutants Kat5-Q377E G380E and Kat5-Y47A, induces severe chromosomal instability (CIN) during trophoblast cells division, leading to embryonic lethality. Moreover, mutation of a key lysine acetyltransferase 5 (KAT5) substrate, H2A.Z, via the introduction of H2az1-K5R K8R K12R K14R (which prevents H2A.Z acetylation), phenocopies the effects of KAT5 loss. Integrated RNA sequencing and CUT&Tag in mouse trophoblast stem cells reveal that KAT5, through H2A.Z acetylation, regulates transcription of key mitotic genes (Aurka, Aurkb, and Cenpa). We extend our finding to human trophoblast stem cells, demonstrating a conserved role for KAT5 in preventing CIN. Clinical analysis of placental villi from recurrent pregnancy loss patients with copy number variations revealed reduced expression of KAT5 and acetylated H2A.Z. This study demonstrates that the conserved KAT5-H2A.Z acetylation pathway safeguards chromosomal stability in trophoblast cells, supporting placenta development and successful pregnancy.