Three-dimensional (3D) cell culture enhanced cells-cells communication, promoting developmental processes and influencing cell performance. In this study, 3D alginate-gelatin core–shell capsules (AGC) were fabricated by using a microfluidic device. Human osteoblast-like MG-63 cells were encapsulated within the 3D model. The morphology and physicochemical properties of the AGC were characterized by using scanning electron microscopy (SEM), Flourier Transform Infrared Spectrum (FTIR), Gravimetric thermal analyzer (TGA). The mRNA levels of osteogenetic gene markers were measured by quantitative real-time RT-PCR. The result of a 9.6% weight loss after a 7-day soaking indicates that the AGC exhibited excellent stability. The encapsulated MG-63 cells formed clusters alongside the core of AGC and obtained 200% cell viability after 21-day long-term cultivation. Compared to traditional 2D cell culture, the 3D cultured MG-63 cells performed higher alkaline phosphatase (ALP), a 9.3-fold increase of calcium mineralization activity, and enhanced osteogenic gene expression of BGLAP, COL1A1, and Runx2. These observations suggested that AGC obtains the potential as an ideal 3D microenvironmental cell culture system for biomedical application.