Provided are a cell co-culture apparatus (1) and a method of co-culturing and isolating cells using the cell co-culture apparatus (1) to research an interaction between the cells by direct contact. The cell co-culture apparatus (1) includes a first substrate (10) having a plurality of projections (12) on the surface (11) of the first substrate (10), wherein the projections (12) have top surfaces (13) for culturing cells; a second substrate (20) having the same number of channels (21) as the number of the projections (12) of the first substrate (10) such that the channels (21) fit with the projections (12) of the first substrate (10); and a third substrate (30) having a plurality of channels (31) corresponding with the top surfaces (13) of the projections (12) of the first substrate (10) and a plurality of channels (21) corresponding with the substrate surface (22) between the channels (21) of the second substrate (20).
