Chlorogenic acid has been widely reported to profoundly influence preadipocyte differentiation but without consensus being achieved. In the current study, 3 T3-L1 preadipocytes were differentiated using adipogenic cocktail with or without chlorogenic acid. The influences of chlorogenic acid on the mRNA, lipid and phospho-kinase profiles were evaluated using transcriptomic analysis, lipidomic analysis and phospho-kinase array assay. The obtained results showed that chlorogenic acid treatment during 3T3-L1 cells differentiation altered a series of genes transcription, resulted in obvious changes in the contents of various lipids, and inhibited phosphorylation of several adipogenesis-related kinases. Overall, the observed changes in transcriptomic, lipidomic and phospho-kinase profiles in the current study favor the findings that chlorogenic acid may inhibit the differentiation of 3T3-L1 preadipocytes. In conclusion, the findings from this study highlighted the therapeutic potential of chlorogenic acid for the treatment of obesity.