Fengtong multifloral honey is produced in the “Fengtong Apis cerana Fabr. Genetic Resource Conservation Area,” located in the selenium-rich region of Wanyuan, Dazhou, Sichuan province. It is a certified product under the Geographical Indication system of China for agricultural products. In this work, the flavor characteristics, chemical composition, and bioactivities of Fengtong multifloral honey were investigated. A total of 34 compounds were detected using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). The key flavor substances of Fengtong multifloral honey are dodecanal, decanal, 2-undecanone, 2-nonanone, phenyl-acetaldehyde, and 1-nonanol, giving the honey sweet and floral flavors. In particular, high-altitude samples also possess a rose aroma. The selenium content of Fengtong multifloral honey is 22 μg/kg, and the total phenolic content ranges from 0.63 to 0.72 mg GAE/g, while the total flavonoid content is 0.26~0.31 mg RE/g. A total of 95 compounds were identified using ultra-performance liquid chromatography-electrospray ionization time-of-flight tandem mass spectrometry (UPLC-ESI-TOF-MS/MS) combined with widely targeted metabolomics. The non-sugar compounds commonly detected in all samples were interiotherins A, deoxyneocryptotanshinone, ellagic acid, quercetin 3-sulfate, and isostearic acid. Auraptene and ostruthin were only identified in high-altitude samples, while 2α, 3β-dihydroxdeoxypterodontic acid was found in low-altitude samples. Remarkable antioxidant activities were noted in all Fengtong multifloral honey samples, with IC50 values for DPPH and ABTS+ radical scavenging and a ferric reducing antioxidant power of 0.79~0.82 g/mL, 0.27~0.30 g/mL, and 2.84~3.75 mmol/100 g, respectively. In summary, Fengtong multifloral honey is selenium-containing honey produced by Apis cerana Fabr. with abundant flavonoids, phenolic acids, and terpenes, and remarkable antioxidant activities. These findings offer data support for the development of Fengtong honey products and their quality control standards.