<p>The regulation of germline-associated processes during early embryogenesis is an important aspect of gonadal development in aquaculture species. Here, we employed bath-immersion delivery of a <i>nanos</i>-targeting Morpholino-Vivo (<i>nanos</i>-MO-Vivo) during embryogenesis to transiently disrupt early germline development in the Pacific oyster <i>Crassostrea gigas</i>. Post-fertilization immersion with 100 µM <i>nanos</i>-MO-Vivo for 6&#xa0;h achieved effective repression of germline markers while maintaining acceptable embryo viability. Transcriptomic analyses at the blastula stage revealed coordinated downregulation of PGC markers (<i>vasa</i>, <i>Piwil1</i>) and germline-associated regulatory pathways. Long-term rearing revealed that transient embryonic perturbation of <i>nanos</i> resulted in persistent impairment of adult gonadal development, characterized by reduced gonadal coverage and diminished gametogenic tissue. In silico analysis based on single-cell transcriptomic data further supported <i>nanos</i>-associated regulatory effects within the PGC population. High sequence conservation of nanos among <i>Crassostrea</i> species was accompanied by comparable knockdown responses in <i>C. angulata</i> and <i>C. nippona</i>, suggesting the observed effects are not restricted to a single oyster species. This study links transient embryonic perturbation of germline-associated regulation to long-term gonadal phenotypes, providing insight into reproductive modulation in molluscan aquaculture.</p>