To research the paracrine role of adipose tissue-derived mesenchymal stem cells (ADMSCs) in promoting angiogenesis under the three-dimensional culture conditions consisting of a functionalized self-assembling peptide nanofiber hydrogel. ADMSCs were isolated, extracted, and then identified. Three kinds of peptides (RADAI-16, RGD, and KLT) were prepared, and a functionalized self-assembling peptide nanofiber hydrogel was produced by mixing RADAI-16, RGD, and KLT in a volume ratio 2:1:1. AFM was used to observe RADAI-16, RGD, KLT, and the functionalized self-assembling peptide nanofiber hydrogel. Then, ADMSCs were cultured under three-dimensional conditions consisting of the peptide nanofiber hydrogel, and AFM was used to observe cell migration. The ADMSCs in the common culture group (37°C, 5% CO2 cell culture box) and hypoxic culture group (37°C, 10% CO2, and 1% O2 hypoxic culture box) acted as controls. ADMSCs were three-dimensionally cultured in situ for 1 day, and then the concentrations of HGF and VEGF in the supernatant were determined by ELISA. Cells were extracted from the peptide nanofiber hydrogel, and HO-1 expression was detected by western blotting. ADMSCs have high expression levels of CD29, CD90, and CDl05 and low expression levels of CD34 and CD45. In addition, they can differentiate into adipocytes and osteocytes. The diameters of the fibers of RADAI-16, RGD, KLT, and the functionalized self-assembling peptide hydrogel are 17.34 ± 1.82, 15.50 ± 1.41, 13.77 ± 1.18, and 20.26 ± 1.25 nm, respectively. AFM indicated that cells in the functionalized self-assembling peptide nanofiber hydrogel migrated farther than those in RADAI-16. The concentrations of HGF under common, hypoxic, and three-dimensional culture conditions were 47.31 ± 6.75, 247.86 ± 17.59, and 297.25 ± 17.95 pg/mL, respectively, while the concentrations of VEGF were 218.30 ± 3.03, 267.13 ± 4.27, and 289.14 ± 3.11 pg/mL, respectively. Both HGF and VEGF were expressed more in the presence of the functionalized self-assembling peptide nanofiber hydrogel than in its absence (P < 0.05). Using western blotting, ADMSCs cultured under hypoxic and three-dimensional conditions were found to have high expression levels of HO-1. Culturing ADMSCs under three-dimensional conditions consisting of functionalized self-assembling peptide nanofiber hydrogels can promote their paracrine role in angiogenesis, such as HGF and VEGF, and hypoxia is one of the important elements.