<p>The razor clam <i>Sinonovacula constricta</i> supports intensive aquaculture, yet how its growth responds to sediment organic matter (OM_S) enrichment (a ubiquitous stressor in bivalve culture) is unresolved. Moderate OM_S can benefit filter-feeding bivalves by supplementing food supply, yet excessive enrichment degrades sediment quality and triggers stress to bivalves; however, the threshold levels and key pathways governing growth impacts remain unresolved. Here, we reared juveniles for 35&#xa0;days along an OM_S gradient (14 − 44&#xa0;mg&#xa0;g⁻¹ dw) to determine the OM_S threshold constraining juvenile <i>S. constricta</i> growth and resolve the underlying mechanisms. The results revealed a critical OM_S threshold existed near 36 − 38&#xa0;mg&#xa0;g⁻¹ dw: below this value, growth performance (e.g., wet weight and survival) was indistinguishable from controls; above it, growth declined and mortality rose. Elevated porewater un-ionized ammonium further suppressed growth via direct toxicity. Further, elevated OM_S lowered dissolved oxygen by stimulating nitrification and aerobic mineralization, forcing juvenile <i>S. constricta</i> to shift from aerobic metabolism to inefficient anaerobic glycolysis (as indicated by elevated hexokinase and lactate dehydrogenase activities), thereby inducing physiological stress. Concurrently, hypoxic high-OM_S sediments promoted sulfate reduction and sulfide accumulation, synergistically exacerbating hypoxia toxicity and elevating mortality. High OM_S also reduced gut microbial diversity and enriched opportunistic pathogens (e.g., <i>Vibrio</i>) of juvenile <i>S. constricta</i>, potentially increasing disease susceptibility. Meanwhile, systemic oxidative stress was accompanied by down-regulation of key immune genes, compromising juvenile <i>S. constricta</i> defense. Our findings provide a mechanistic framework for managing sediment OM_S in intensive clam culture, reconciling the contradiction between aquaculture industry and environmental sustainability.</p>