Aggregating into multicellular spheroids within alginate–poly-L-lysine–alginate (APA) microcapsules is important in maintaining the cellular viability and specific functions. However, in the absence of a vascular network, cells in the core of large-sized spheroids are gradually necrotic because of oxygen transfer limitations. In this study, a novel APA microcapsule embedded with three-dimensional fibrous scaffolds (called APA-FS) was proposed to eliminate cellular necrosis by regulating cells to form multi-small spheroids. HepG2 cells were embedded within the APA-FS to form spheroids and the state of these spheroids was evaluated via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazoliumbromide assay, glucose/lactate metabolism, live/dead staining, and hematoxylin and eosin staining. Comparing with the conventional APA microcapsules, the cells within APA-FS organized into multi-small spheroids. The size of these spheroids depended on the concentration of fibrous scaffolds embedded within the microcapsules. In the APA-FS embedded with 5% (v/v) fibrous scaffolds, the average size of cellular spheroids was controlled below 100 microm and the cellular viability was increased by 50% than the control. The results of live/dead staining and hematoxylin and eosin staining showed that the improved cellular viability might be attributed to the decreased necrosis in the core of these spheroids. The improved viability of cells demonstrated the efficiency of this technology. These findings implied that this system might provide a more suitable culture environment for a variety of tissue engineering applications.