Hippophae rhamnoides L. (Elaeagnaceae), commonly known as “Sea buckthorn” and “Vitamin tree”, is a spiny deciduous shrub whose fruit is known for its nutritional composition, such as vitamin C, and is consumed as a dietary supplement worldwide. As part of our ongoing efforts to identify structurally new and bioactive constituents from natural resources, the phytochemical investigation of the extract of H. rhamnoides fruits led to the isolation of one malate derivative (1), five citrate derivatives (2–6), and one quinate derivative (7). The structures of the isolated compounds were elucidated by analysis of 1D and 2D nuclear magnetic resonance (NMR) spectroscopic data and high-resolution electrospray ionization (HR-ESI) liquid chromatography–mass spectrometry (LC/MS) data. Three of the citrate derivatives were identified as new compounds: (S)-1-butyl-5-methyl citrate (3), (S)-1-butyl-1′-methyl citrate (4), and (S)-1-methyl-1′-butyl citrate (6), which turned out to be isolation artifacts. The absolute configurations of the new compounds were established by quantum chemical electronic circular dichroism (ECD) calculation, which is an informative tool for verifying the absolute configuration of organic acid derivatives. The isolated compounds 1–7 were evaluated for their stimulatory effects on osteogenesis. Compounds 1, 3, 4, 6, and 7 stimulated osteogenic differentiation up to 1.4 fold, compared to the negative control. These findings provide experimental evidence that active compounds 1, 3, 4, 6, and 7 induce the osteogenesis of mesenchymal stem cells and activate bone formation.