Gastrulation is a universal process in the morphogenesis of many animal embryos. In sea urchin embryos, it involves the invagination of a single-layered vegetal plate into the blastocoel. Although morphological and molecular events in gastrulation have been well studied, the mechanical driving forces and the regulatory mechanism underlying gastrulation is not fully understood. In this study, structural features and cytoskeletal distributions were studied in sea urchin embryos using an “exogastrulation” model induced by inhibiting the H+/K+ ion pump with omeprazole. The vegetal poles of the exogastrulating embryos showed reduced roundness indices, intracellular pH polarization, and intracellular F-actin polarization at the pre-early gastrulation stage compared with normal embryos. Gastrulation stopped when F-actin polymerization or degradation was inhibited via RhoA or YAP1 knockout, although pH distributions were independent of such a knockout. A mathematical model of sea urchin embryos at the early gastrulation reproduced the shapes of both normal and exogastrulating embryos using cell-dependent cytoskeletal features based on F-actin and pH distributions. Thus, gastrulation required appropriate cell position-dependent intracellular F-actin distributions regulated by the H+/K+ ion pump through pH control.