Lead (Pb) is one of the ubiquitous and toxic elements in aquatic environment. In oysters, gills and digestive glands are the main target organs for Pb-induced toxicity, but there is limited information on the molecular mechanisms underlying its toxicity. The present study investigated the Pb-induced toxicity mechanisms in the Pacific oyster (Crassostrea gigas) based on transcriptome, phenotypic anchoring, and validation of targeted gene expression. Gene ontology and pathway enrichment analyses revealed the differential Pb toxicity mechanisms in the tissues. In the gills, Pb disturbed the protein metabolism, with the most significant enrichment of the "protein processing in endoplasmic reticulum" pathway. The main mechanism comprised of a Pb-stimulated calcium (Ca2+) increase by the up-regulation of transporter-Ca-ATPase expression. The disturbed Ca2+ homeostasis then further induced high expressions of endoplasmic reticulum (ER) chaperones, leading to ER stress in the oysters. Unfolded proteins induced ER associated degradation (ERAD), thereby preventing the accumulation of folding incompetent glycoproteins. However, Pb mainly induced oxidative reduction reactions in the digestive gland with high accumulation of lipid peroxidation products and high expression of antioxidant enzymes. Further, Pb induced fatty acid beta-oxidation and CYP450 catalyzed co-oxidation due to increased metabolic expenditure for detoxification. The increased content of arachidonic acid indicated that Pb exposure might alter unsaturated fatty acid composition and disturb cellular membrane functions. Taken together, our results provided a new insight into the molecular mechanisms underlying Pb toxicity in oysters.