Alternative splicing (AS) is a pivotal biological process that enhances transcriptomic plasticity in eukaryotes, especially under environmental stress. In this study, we integrated PacBio Iso-Seq and Illumina RNA-seq technologies to characterize the full-length transcriptome of Chlamydomonas reinhardtii under dark anaerobic conditions. Anaerobic treatment was associated with extensive remodeling of transcript structures, with intron retention emerging as the predominant splicing type. Transcript-structure changes were concentrated in genes related to carbon metabolism, pyruvate conversion, and fatty acid biosynthesis. Several key genes showed clear condition-dependent transcript isoform changes, including putative isoform switching events, which were further supported by qRT-PCR analysis. These findings support the view that AS-associated transcript-structure remodeling contributes to the anaerobic response of Chlamydomonas reinhardtii and provide a high-quality transcriptomic resource for future studies of stress adaptation and gene regulation in green algae.