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<i>Morus</i> spp. leaves (MSLs) show various beneficial effects in the treatment of metabolic-related diseases, which have created a growing interest in MSL development as dietary supplements and functional foods. The illustration of chemical compositions and screening of high-quality MSL resources are therefore necessary for further application. This study developed a new UHPLC-ESI-QTOF-MS/MS strategy of in-source collision-induced dissociation (IS-CID) and target collision-cell CID (TCC-CID) to quickly capture analogues with consistent skeleton, and combined global natural product social molecular networking (GNPS) to efficiently annotate bioactive phytochemicals in MSLs. For the results, 49 bioactive ingredients, including quercetin-type flavonoids, kaempferol-type flavonoids, chlorogenic acid isomers, 1-deoxynojirimycin, <i>γ</i>-aminobutyric acid, amino acids, and unsaturated fatty acids, were systematically identified in MSLs for the first time. Quantification for the typical components was simultaneously carried out in MSLs of 90 <i>Morus</i> resources collected from different locations. Partial least squares discriminant analysis (PLS-DA) indicated that quercetin-3-<i>O</i>-(6″-<i>O</i>-malonyl)-glucoside, rutin, kaempferol-3-<i>O</i>-(6″-<i>O</i>-malonyl)-glucoside, kaempferol-3-<i>O</i>-rutinoside, and chlorogenic acid showed high variable importance in the project (VIP > 1) that were significant constituents for the differences between MSL species. Then, high-quality MSLs were comprehensively screened in multiple <i>Morus</i> cultivars based on the criteria importance through intercriteria correlation (CRITIC) method. This study presented an efficient strategy to annotate bioactive compounds, revealed the difference of bioactive components in MSLs, and provided important information for the high-value production of <i>Morus</i> cultivars in food and supplement fields.