The present work aimed to explore the molecular mechanisms and candidate genes associated with fat metabolism in Anqingliubai (obese) and Yorkshire (lean) pigs. The transcriptome profiling of backfat between Anqingliubai and Yorkshire pigs was carried out by RNA-sequencing technology. The sum of clean reads were 288.3 and 365.3 million which was obtained from the RNA sequencing data in the Anqingliubai and Yorkshire pigs, respectively. Most reads were located in exonic region, while less reads were located in intergenic and intronic regions. There were 2601 upregulated genes, but 284 downregulated genes in Yorkshire pigs compared with those in Anqingliubai pigs. The top 10 most significant Gene Ontology (GO) terms included catalytic activity, binding, cell, cytoplasm, positive regulation of multicellular organismal process, biological regulation, cellular process, etc. There were 54 significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including cytokine-cytokine receptor interaction, biosynthesis of unsaturated fatty acids, fatty acid metabolism, regulation of lipolysis in adipocytes, glycerolipid metabolism, etc. The results of differentially expressed genes from sequence were highly reliable by qRT-PCR confirmation. The present work will help understanding of the different mechanisms involved in fat deposition between lean and obese pigs.