Isoprene from marine emissions significantly influences the atmospheric oxidative capacity and secondary pollutants in the marine boundary layer. While marine algae are recognized as primary contributors to marine emissions of isoprene, the long-term and dark-phase isoprene production from these organisms remains underexplored, potentially lead to inaccuracies in estimating marine isoprene emissions. In this study, we conducted a time series investigation of isoprene emission from Chaetoceros curvisetus with a growth cycle duration of 19 days and examined the influence of environmental factors. Our findings revealed that C. curvisetus emits isoprene during its whole growth cycle, with peak emissions (2.82 × 10−11 μmol cells−1 h−1) recorded in the stationary phase. Under nitrogen, light and temperature stress, significant release of isoprene is found. During both the light and dark phases, isoprene emission was observed with comparable intensities. Transcriptome analysis showed that 41 differentially expressed transcripts were involved in the synthesis of volatile organic compounds. Notably, downregulation of genes associated with pyruvate synthesis in the glycolysis pathway suggests its importance for dark isoprene release. The study also highlighted downregulation of isopentenyl phosphate kinase and Gene Ontology enrichment in organelles housing mevalonate (MVA) pathways, suggesting that exchange involving the transport of intermediate metabolites between MVA and methylerythritol phosphate (MEP) pathway may contribute to the released isoprene in dark phase. Furthermore, the synthesis of substrates and downstream products is related to the dark release of isoprene. In conclusion, our study illuminates the pivotal roles of substrate availability, interplay between MVA and MEP pathways, and glycolysis pathway in governing isoprene emissions under light/dark cycles.