Metastasis is a primary cause of mortality and treatment failure in ovarian cancer, with limited effective therapeutic strategies. Low-intensity ultrasound (LIUS) and microbubbles (MBs) has been demonstrated as an adjunctive technique capable of enhancing drug delivery and suppressing tumor metastasis. However, the underlying mechanisms remain incompletely understood. In this study, we aimed to investigate whether LIUS + MBs alone could suppress tumor metastasis and to explore its mechanism of action through disruption of the cytoskeletal remodeling in filopodia, an essential structure in the early stages of cancer cell dissemination. Based on cell-based experiments to determine the optimal parameters, our results showed LIUS + MBs significantly inhibited the migration and invasion of ovarian cancer cells. In vivo, LIUS + MBs treatment markedly suppressed the overall metastasis in the orthotopic ovarian cancer model, and in both the intraperitoneal and hematogenous metastatic models established by injecting pretreated cells. Morphologically, such treatment led to a notable reduction in the length and number of filopodia, while the number of lamellipodia remained unaffected. At the molecular level, LIUS + MBs disturbed filopodia formation and the metastatic potential of ovarian cancer cells by suppressing the activation of Cdc42, a key regulator of cytoskeletal dynamics. The inhibitory effect was reversed by the overexpression of Cdc42CA. Further proteomic and bioinformatics analysis implied that LIUS + MBs may reduce Cdc42 activity by upregulating the expression of GTPase-activating proteins (GAPs). Our research provides novel insight into the mechanism by which LIUS + MBs can inhibit tumor metastasis, highlighting its role in disturbing the Cdc42-mediated cytoskeletal remodelling of filopodia.