Shuxuening injection (SXNI) is the pharmaceutical preparations of Ginkgo biloba for treating coronary heart disease, stenocardia and ischemic cerebrovascular disease. In order to guarantee the clinical efficacy and drug safety, the chemical and biological variation of SXNIs from different manufacturers should be monitored and controlled. In this study, a strategy for the quality control of SXNIs was established. A widely targeted metabolomics method based on scheduled MRM (sMRM) was developed and 86 compounds with good linearity, sensitivity, and repeatability was selected for relative quantitation to reveal the chemical variation among 7 SXNI manufactures. 10 compounds with big content variation among different manufactures were screened out, which should be used to control the uniformity of SXNIs. Then the correlation analysis of the chemical variation with bioactivity and pharmacology analysis showed that 8 compounds relating with the bioactivity should also be served as the quality control index. The application of widely targeted metabolomics based on UPLC-sMRM and bioactivity analysis could offer multi-dimensional data for holistic quality evaluation of traditional Chinese medicine (TCM).