Microwell chip culture is a promising technique for the generation of homogenous spheroids. We investigated the relationship between the structure of the bottom surface of microwell chip and the properties of HepG2 spheroid. We developed a microwell chip, the bottom surface of which consisted of a honeycomb-patterned polymer film (honeycomb film) that had a regular porous structure (HF chip). The chip comprised 270 circular microwells; each microwell was 600 μm in diameter and 600 μm in depth. At the center of the honeycomb film, an area, 200 μm in diameter, was modified with collagen to facilitate cell adhesion. With the exception of the collagen-coated area, the entire microwell was modified with polyethylene glycol to eliminate cell adhesion. HepG2 cells formed uniform spheroids when cultured in the microwells of HF chip. Furthermore, the cells passed through the porous structure of honeycomb film and formed spheroids at its opposite side. The spheroid growth of HepG2 cells cultured in HF chip was greater than that when the cells were culture in a microwell chip, the bottom surface of which was made of poly-methylmethacrylate (PMMA chip). The albumin secretion activity of HepG2 spheroids in HF chip was equal to that in PMMA chip. These results indicate that the microwell bottom with a porous structure enhances the cell growth and maintains well the spheroid function. Thus, HF chip is a promising platform for spheroid cell culture.