A cell incubating apparatus and a method of culturing cells in vitro are disclosed, which relates to medical cell proliferation, pharmaceutical chemical screening and automatic cell analysis in tissue engineering technology. The apparatus establishes an imitating three-dimensional transportation microenvironment by assembling a top plate, a bottom plate and at least one culture plate apparatus for incubating cells. The apparatus is not only for incubating the tissue specific cells with biological function but also for lowering the cost of culturing cells for personal medical use.