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Clonorchis sinensis is a significant zoonotic food-borne parasite that causes a range of hepatobiliary diseases, which in severe cases can even lead to cholangiocarcinoma. To explore new diagnostic and treatment strategies, the dynamic RNA regulatory processes across different developmental stages of C. sinensis were analyzed by using whole-transcriptome sequencing. The chromosomal-level genome of C. sinensis was used for sequence alignment and annotation. In this study, we identified a total of 59,103 RNAs in the whole genome, including 2,384 miRNAs, 25,459 mRNAs, 27,564 lncRNAs and 3,696 circRNAs. Differential expression analysis identified 6,556 differentially expressed mRNAs, 2,231 lncRNAs, 877 miRNAs and 20 circRNAs at different developmental stages. Functional enrichment analysis highlighted the critical role of microtubule-related biological processes in the growth and development of C. sinensis. And coexpression analysis revealed 97 lncRNAs and 85 circRNAs that were coexpressed with 42 differentially expressed mRNAs that associated with microtubules at different developmental stages of C. sinensis. The expression of the microtubule-related genes dynein light chain 2 (DLC2) and dynein light chain 4 (DLC4) increased with C. sinensis development, and DLC2/4 could be inhibited by albendazole. Finally, by constructing competing endogenous RNA (ceRNA) networks, the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA regulatory relationships were constructed, and the ceRNA networks of MSTRG.14258.5-novel_miR_2287-newGene_28215 and MSTRG.14258.5-novel_miR_2216-CSKR_109340 were verified. This study suggests, through whole transcriptome sequencing, that the context of microtubule regulation may play an essential role in the development and growth of C. sinensis. Author summary: This study is the first to comprehensively elucidate the entire transcriptome of Clonorchis sinensis by exploring the expression and regulatory dynamics of noncoding RNAs and mRNAs at different developmental stages in its life cycle. By using next-generation sequencing technology, this research demonstrated new mRNAs, miRNAs, lncRNAs and circRNAs, and established valuable resources for future parasitic research. Compared with mRNAs, lncRNAs have shorter gene lengths, lower expression levels, fewer exons and fewer isoforms. Differential expression analysis demonstrated stage-specific patterns of noncoding RNAs and mRNAs in C. sinensis during its life cycle, thus providing crucial insights into the role of noncoding RNAs in parasite growth and development. Furthermore, the construction of ceRNA regulatory networks revealed that microtubule-related lncRNAs and circRNAs in C. sinensis may play an important role in its growth and development. This study advances our understanding of the entire transcriptome of C. sinensis and introduces novel perspectives for future parasitic infection treatment strategies. In summary, this study establishes a foundation for in-depth investigations into the interplay between noncoding RNAs and parasites, as well as the associated biological processes, thus demonstrating broad research and therapeutic potential. [ABSTRACT FROM AUTHOR]