A novel method of making microcapsules in a macrocapsule is demonstrated as a 3-D culture system in this article. Mouse embryonic stem (mES) cells as model cells were used in the 3-D culture space, and the cell viability and histological observation were conducted. Furthermore, Oct4 gene expression was evaluated for the undifferentiated status of mES cells in this 3-D model. The results showed that mES cells can grow in this 3-D model and retain their normal viability and morphology. This 3-D model allows mES cells to stay in the undifferentiated state better than 2-D culture systems. This work demonstrates a new 3-D tissue model which can provide an in vivo like microenvironment for non-differentiated mES cells with good immunoisolation. This approach may bridge the gap between traditional 2-D cell culture and animal models.