Colorectal cancer (CRC), the third leading cause of cancer-related deaths, is increasingly affecting younger populations. However, the molecular events and gene regulation underlying formation of CRC remain largely unexplored. Here, leveraging the latest long-read sequencing technologies, we have comprehensively profiled colonic polyps and CRC across key developmental stages. We uncover novel molecular signatures associated with CRC progression, focusing on RNA isoform diversity, genetic mutations, and epigenetic changes. Specifically, we employ PacBio’s latest technologies, including the Kinnex single-cell RNA and whole genome sequencing on the Revio platform. Analysis of four disease stages (normal, benign polyp, dysplastic polyp, adenocarcinoma) in individuals with Familial Adenomatous Polyposis (FAP) enables a comprehensive characterization of splicing alterations and their correlation with somatic mutations and methylation dynamics. Furthermore, we apply spatial transcriptomic assays to localize specific aberrant transcripts and define their tissue neighborhood in situ. This effort generates unprecedented multi-modal datasets, facilitating actionable therapeutic discovery and significantly advancing our understanding of CRC progression from pre-cancer to malignancy.