Background/Objectives: Vitex negundo L. is a multi-part medicinal and aromatic plant, but organ-resolved chemical information for its aerial organs remains incomplete. This study generated an exploratory paired untargeted liquid chromatography–tandem mass spectrometry (LC-MS/MS) dataset for flowers, stems, and leaves and prioritized organ-associated putative metabolite families for subsequent validation. Methods: To reduce inter-individual background variation, flower, stem, and leaf tissues were harvested from the same three V. negundo individuals to form n = 3 paired plant blocks. LC-MS/MS feature data were filtered using pooled quality-control relative standard deviation (QC RSD ≤ 30%), median-normalized and log2-transformed. Principal component analysis (PCA) provided an unsupervised overview, and paired feature-level comparisons were performed using paired t-tests with Benjamini−Hochberg false discovery rate (FDR) correction. Results: A total of 42,125 QC-filtered LC-MS features were retained. PCA showed organ-associated separation among flowers, stems, and leaves. Using FDR < 0.05 and |mean paired log2 difference| ≥ 1, paired screening yielded 13,043, 22,836, and 13,393 FDR-supported LC-MS features for flower vs. stem, flower vs. leaf, and stem vs. leaf comparisons, respectively. Higher-scoring putative annotations suggested organ-associated putative family-level patterns, including flavonoid-related, hydroxycinnamic-acid derivative, phenolamide-related, triterpenoid-related, iridoid-related, and lignan-related signals. Conclusions: This organ-resolved dataset provides a chemical-feature framework for V. negundo aerial organs and putative family-level patterns for future structural confirmation, targeted quantification, bioactivity evaluation, and quality-marker development. Feature counts are not equivalent to unique metabolite counts, and compound labels require validation before being interpreted as confirmed structures.