Spns1 [Spinster homolog 1 (Drosophila)] in vertebrates, as well as Spin (Spinster) in Drosophila, is a hypothetical lysosomal H+-carbohydrate symporter, which functions at a late stage of macroautophagy (hereafter autophagy). The Spin/Spns1 defect induces aberrant autolysosome formation that leads to developmental senescence in the embryonic stage and premature aging symptoms in adulthood. However, the molecular mechanism of the specific pathogenesis still awaits elucidation. Using chemical genetic and CRISPR/Cas9-mediated genome-editing approaches in zebrafish, we investigated a mechanism that ameliorates Spns1 loss-mediated embryonic senescence as well as autolysosomal impairment. Unexpectedly, we identified the vacuolar-type H+-ATPase (v-ATPase) subunit gene, atp6v0ca (ATPase, H+ transporting, lysosomal, V0 subunit ca) as a spatiotemporal suppressor for senescence induced by the loss of Spns1, while the sole loss of Atp6v0ca led to senescent embryos. Moreover, we discovered that the concurrent heritable defect of both spns1 and atp6v0ca still induced premature autophagosome-endosome and autophagosome-lysosome fusion without sufficient acidity in the lysosome. Our data suggest that Spns1 and the v-ATPase orchestrate proper endo-lysosomal biogenesis with optimal acidification that is critically linked to developmental senescence and survival.