SummaryDe novo shoot organogenesis is an important biotechnological tool for fundamental studies in plant. However, it is difficult in most bamboo species, and the genetic control of this highly dynamic and complicated regeneration process remains unclear. In this study, based on an in‐depth analysis at the cellular level, the shoot organogenesis from calli of Ma bamboo (Dendrocalamus latiflorus Munro) was divided into five stages. Subsequently, single‐molecule long‐read isoform sequencing of tissue samples pooled from all five stages was performed to generate a full‐length transcript landscape. A total of 83 971 transcripts, including 73 209 high‐quality full‐length transcripts, were captured, which served as an annotation reference for the subsequent RNA sequencing analysis. Time‐course transcriptome analysis of samples at the abovementioned five stages was conducted to investigate the global gene expression atlas showing genome‐wide expression of transcripts during the course of bamboo shoot organogenesis. K‐means clustering analysis and stage‐specific transcript identification revealed important dynamically expressed transcription regulators that function in bamboo shoot organogenesis. The majority of abiotic stress‐responsive genes altered their expression levels during this process, and further experiments demonstrated that exogenous application of moderate but not severe abiotic stress increased the shoot regeneration efficiency. In summary, our study provides an overview of the genetic flow dynamics during bamboo shoot organogenesis. Full‐length cDNA sequences generated in this study can serve as a valuable resource for fundamental and applied research in bamboo in the future.