Organ regeneration is becoming a promising choice for many patients; however, many details about the mechanisms underlying organ regeneration remain unknown. As regenerative organs, hair follicles offer a good model to study the mechanisms associated with regenerative medicine. The relevant studies have mainly focused on donor cells, and there are no systematic studies involving the effect of host factors on hair follicle reconstruction. Thus, we intend to explore the effect of host cells on hair follicle reconstruction. Epidermal and dermal cells from red fluorescent protein (RFP) transgenic newborn mice were injected into green fluorescent protein (GFP) transgenic mice. In addition, we wrapped the mixed dermal and epidermal cells from GFP transgenic and RFP transgenic mice by the Cell-in-a-Box kit to form "capsules," so that the cells within would be isolated from host cells. These capsules were cultured in vitro and transplanted in vivo. Fully developed reconstructed hair follicles were observed after the injection of mixed cells. These reconstructed follicles mainly consisted of donor cells, as well as a small number of host cells. The encapsulated cells gradually aggregated into cell spheres in vitro without apparent differentiation towards hair follicles. With respect to the transplanted capsules, concentric circle structures were observed, but no hair follicles or hair shafts formed. When the concentric circle structures were transplanted in vivo, mature hair follicles were observed 30 days later. Host cells were found in the reconstructed hair follicles. Thus, we conclude that host cells participate in the process of hair follicle reconstruction, and they play a vital role in the process, especially for the maturation of reconstructed hair follicles. Furthermore, we established a special hair follicle reconstruction system with the help of capsules: transplant cells were isolated from host, but other factors from host could exchange with cells inside.