Merchants used frozen chicken to pass it off as chilled chicken, resulting in Economically Motivated Adulteration incidents. Here in this work, firstly, we established OPLS-DA and OPLS-R models based on metabolomics to obtain differential metabolites in chilled and frozen chicken (with different storage times), the PLS-DA model based on above differential compounds could achieve accuracy of 91% (training) and 100% (testing) for the adulteration identification of uncooked chilled and frozen chicken. Secondly, cooking study was carried out to identify the discrepancy of the cooked chilled and frozen chicken. Higher nicotinamide, o-acetyl-l-carnitine, hypoxanthine, and IMP levels indicated better nutrition quality and more desirable flavor in chilled chicken nuggets, while higher bitter and sour peptides in frozen chicken nuggets indicated the loss of freshness.