Under global climate change, the frequency and scale of harmful algal blooms (HABs) including red tides and green tides in coastal waters have been continuously expanding. Most existing studies focus on the adverse ecological impacts of algal blooms, while their potential carbon sequestration capacity is largely overlooked. In this study, Skeletonema costatum (a typical red tide diatom) and Ulva prolifera (the dominant green tide macroalga) were selected as experimental materials. We systematically investigated the independent and interactive effects of ocean warming and nitrogen enrichment on carbon sequestration and carbon storage of the two bloom-forming algae, to fill the research gap in comparative analysis of carbon sequestration responses across different bloom species. The results reveal distinct interspecific differences in algal carbon sequestration responses to warming and nitrogen loading. For Skeletonema costatum, single high-nitrogen treatment significantly promoted the accumulation of particulate organic carbon (POC), whereas isolated warming and combined warming-nitrogen treatments exerted no significant influence on it. High nitrogen alone reduced dissolved organic carbon (DOC) stocks, and warming plus nitrogen co-treatment showed no notable effects. The combined warming and nitrogen enrichment significantly elevated refractory POC (RPOC) production, while refractory dissolved organic carbon (RDOC) accumulation remained unaffected by warming, nitrogen enrichment, or their interaction. Collectively, future concurrent warming and nitrogen overload will hardly alter the carbon fixation efficiency of S. costatum, yet enhance its carbon sequestration potential. For Ulva prolifera, warming alone produced no significant change in POC pools, while single nitrogen enrichment and combined warming-nitrogen treatments both substantially stimulated POC accumulation. DOC concentrations were markedly increased under high-nitrogen conditions at both low and high temperatures, and the coupled warming-nitrogen treatment also boosted DOC production. RPOC accumulation was suppressed by high nitrogen, with no observable impacts from warming or the combined stress. RDOC pools were insensitive to temperature variation, but both high nitrogen and warming-nitrogen co-treatment significantly elevated RDOC yields. Under projected future warming and eutrophication scenarios, both the carbon fixation and carbon storage capacity of U. prolifera will be strengthened. In conclusion, red tide diatoms and green tide macroalgae exhibit divergent response patterns of carbon sequestration processes to warming and nitrogen enrichment. Therefore, distinguished assessments targeting different bloom types are required when evaluating coastal marine carbon budgets.