The present invention relates to a cooling structure of a lithium ion secondary battery system. The cooling structure of a lithium ion secondary battery system according to the present invention provides cooling channels for lithium battery unit cells accommodated by a laterally partitioned arrangement of main frames, each having a heat radiation part and lattice-shaped paths, and partitioning frames, and allows air, blown by a cooling fan, to cool the lithium battery unit cells while passing through the cooling channels and the lattice-shaped paths. Each of the main frames has a pair of passage slots formed in both sides thereof to allow the air blown by the cooling fan to be directly blown to each accommodated lithium battery unit cell, thus forming each secondary cooling channel communicating with the pair of passage slots.