The circadian clock system regulates a wide range of physiological processes in mammals, and the core circadian clock gene Bmal1 is crucial for maintaining the oscillations of circadian clock system by controlling the rhythmic expression of numerous clock-controlled genes. To explore the transcriptional changes associated with Bmal1 deletion in liver tissues, we collected the liver tissues of global and liver-specific Bmal1 knockout mice at two circadian time points (CT2 and CT14), and used them for RNA-seq analysis. Genotyping, Locomotor activity analysis, comprehensive quality control analyses, including base quality scores, GC content, and mapping rate, confirm the high quality of the sequencing data. Furthermore, differential expression and enrichment analyses reveal significant enrichment in circadian rhythm-related pathways, underscoring the reliability and validity of the dataset. These data offer a valuable resource for researchers studying the role of BMAL1 in liver physiology and pathology, as well as the broader field of circadian biology.