Biological control is a key component of integrated pest management (IPM). To suppress pests in a certain threshold, chemical control is used in combination with biological and other control methods. An essential premise for using pesticides in IPM is to ascertain their compatibility with beneficial insects. Chrysopa sinica (Neuroptera: Chrysopidae) is an important predator of various pests and used for pest management. This study was intended to analyze metabolic changes in C. sinica larvae after feeding on azadirachtin-treated Plutella xylostella (Lepidoptera, Plutellidae) larvae through a non-targeted LC–MS (Liquid chromatography–mass spectrometry) “based metabolomics analysis. Results showed that C. sinica larvae did not die after consuming P. xylostella larvae treated with azadirachtin. However, their pupation and eclosion were adversely affected, resulting in an impairment in the completion of their life cycle. Feeding C. sinica larvae with azadirachtin-treated P. xylostella larvae affected over 10,000 metabolites across more than 20 pathways, including the metabolism of amino acids, carbohydrates, lipid, cofactors, and vitamins in C. sinica larvae, of which changes in amnio acid metabolism were particularly pronounced. A working model was proposed to illustrate differential changes in 20 metabolites related to some amino acid metabolisms. Among them, 15 were markedly reduced and only five were elevated. Our results suggest that azadirachtin application may not be exclusively compatible with the use of the predator C. sinica for control of P. xylostella. It is recommended that the compatibility should be evaluated not only based on the survival of the predatory insects but also by the metabolic changes and the resultant detrimental effects on their development.