Background: The Olecranon honey peach shaped like an eagle’s beak. In this study, full-length transcriptome sequencing of the Olecranon honey peach and its bud mutant variant was performed by Oxford Nanopore Technologies to comparatively analyze the differentially expressed genes and the transcriptome to identify important fruit shape-related genes. Results: Full-length transcriptome sequencing was performed to analyze the two peaches. A consensus isoform was obtained and compared to the reference genome for an elimination of redundancy analysis. As a result, a final set of 58 596 transcript sequences was obtained. A total of 21 745 simple sequence repeats were obtained, and 18 322 alternative splicing (AS) events were identified. The comparative analysis of the non-redundant transcript revealed 2530 new gene loci and 37 364 novel transcripts. A total of 457 genes were differentially expressed in the two groups, including 169 up-regulated genes and 288 down-regulated genes. A total of 1519 transcripts were differentially expressed, of which 552 were up-regulated and 997 were down-regulated. Conclusions: In the case of the plant hormone signal transduction pathway identified by the KEGG annotation, our analyses revealed that differential expression of genes 9229 , 26004 , 22504 , 2822 , 2826 , 2824 , ONT.1953 , ONT.1950 , and ONT.1953 was related to the shape of the peach and may regulate the production of large fruit, via endogenous hormones, secondary metabolites, and signal transduction. This study provides useful information on the shape-related genes and transcripts in the Olecranon honey peach.