Apocynum pictum and Apocynum venetum are two medicinal important halophytes' plants from Xinjiang, China. However, honey derived from these plants, remains unexplored. This study investigated the physicochemical properties, essential elements, enzymatic activity, and metabolomic profiles of both types of honeys. This study identified A. pictum honey significantly higher peroxidase (POD) activity (19.2 ± 1.1 U/g vs. 7.5 ± 0.3 U/g), adenine content (17.5 ± 0.1 mg/g vs. 6.2 ± 0.1 mg/g), and protein levels (13.0 ± 0.5 mg/g vs. 11.2 ± 0.4 mg/g) compared to A. venetum honey. Mineral analysis showed potassium (76.5 ± 1.2 mg/L, 2.8 ± 0.1, 46.0 ± 1.5 mg/L), magnesium, and zinc in A. pictum honey, aligning with its adaptation to arid conditions. Total 735 differentially accumulated metabolites (DAMs), such as flavonoids (diosmetin, chrysin), phenolic acids (homogentisate), and alkaloids (tryptamine), linked to antioxidant, anti-inflammatory, and anticancer properties. Thus, approved A. pictum honey superior nutritional and therapeutic values.