Cyprinus carpio var. qingtianensis, commonly known as the Qingtian paddy field carp, is a key species in the Qingtian rice-fish co-culture system. However, the early developmental process has not been sufficiently studied, limiting a comprehensive understanding of its biological mechanisms. In this study, transcriptome sequencing was used to analyze the gene expression dynamics at six key developmental stages: gastrula (TS1), 6-somite (TS2), eye pigmentation (TS3), hatching (TS4), 12 h post-hatching (TS5), and 24 h post-hatching (TS6). In total, 31153 differentially expressed transcripts (DETs) were identified. GO and KEGG enrichment analyses revealed that differentially expressed genes (DEGs) in the TS2vsTS1 stage were mainly enriched in nucleic acid metabolism and cell cycle-related pathways, indicating active cell proliferation during the transition from the blastula stage to somite formation. In TS3vsTS2, upregulated genes were significantly involved in skeletal muscle development and aerobic metabolic processes, suggesting the establishment of muscular and energy metabolism systems. In TS4vsTS3, pathways related to cardiac muscle contraction, neural development, and sensory functions were prominently activated, reflecting functional maturation from organ formation to the pre-hatching stage. The number of DEGs in TS5vsTS4 and TS6vsTS5 was relatively low, mainly involving stress responses and immune functions, indicating a shift toward environmental adaptation after hatching. These results indicated that C. carpio var. qingtianensis follows a "framework first, acceleration later" developmental strategy, in which maternal factors continue to regulate embryonic development even after zygotic genome activation (ZGA). In terms of energy metabolism, Qingtian paddy field carp adapted to the hypoxic rice field environment by downregulating oxidative phosphorylation (OXPHOS) and activating the HIF-1 signaling pathway. Additionally, 16 transcripts related to hatching enzyme (HCE) expression were identified in cluster 6, with all but one annotated as hce1 and hce2, suggesting that hatching in the Qingtian paddy field carp is primarily mediated by HCE activity. This study provides new molecular insights into the early developmental regulation of C. carpio var. qingtianensis revealed its unique adaptations to the rice-fish ecosystem and lays a foundation for further investigation into its regulatory mechanisms.