MolluscDB 2.0 is the most comprehensive multi-omics database for molluscan research, integrating nearly 4,200 datasets from 1,450 species across all eight classes and 92% of orders, with geographic coverage ranging from terrestrial to deep-sea environments. It features 14 upgraded core modules and over 20 customized analytical tools tailored to molluscan biology, all accessible through an integrated genome browser for intuitive visualization of complex omics data. As the largest and most feature-rich open-access platform in the field, MolluscDB 2.0 aims to unravel the evolutionary and biological mysteries of mollusks and support genetic resource exploration and breeding in shellfish.