Fatty acid composition is associated with meat quality in pigs as well as with obesity- and diabetes-related traits in humans. Liver and muscle are important tissues for fatty acid metabolism. In this study, we evaluated correlations between liver and muscle transcriptomes and fatty acid composition traits in muscle and abdominal fat tissues in 335 F2 pigs from a White Duroc × Erhualian F2 pig resource population. Transcripts significantly correlated with fatty acid composition traits were enriched for genes involved in the categories of triglyceride catabolic process, mitochondrial function, hematological and immune system, and disease such as Type II diabetes. Gene co-expression network analysis further identified liver network modules relevant to fatty acid unsaturation index that were enriched in platelet activation and the type I interferon signaling pathway and highlighted the connections between variations in fatty acid composition and genes involved in hematological and immune system. Integrative analysis of the expression QTL identified ELOVL6 and SCD as plausible candidate genes underlying the loci for muscle C18:1n-9/C16:1n-7 values on chromosome 8 and the loci for muscle C18:1n-9/C18:0 contents on chromosome 14 respectively.