Abstract. Let F n be a free group of rank n and F N n the quotient group of, where Γ n (k) denotes the k-th subgroup of the lower central series of the free group F n . In this paper, we determine the group structure of the graded quotients of the lower central series of the group F N n by using a generalized Chen's integration in free groups. Then we apply it to the study of the Johnson homomorphisms of the automorphism group of F n . In particular, under taking a reduction of the target of the Johnson homomorphism induced from a quotient map F n → F N n , we see that there appear only two irreducible components, the Morita obstruction S k H Q and the Schur-Weyl module of type H, in the cokernel of the rational Johnson homomorphism τ k,Q = τ k ⊗ id Q for k ≥ 5 and n ≥ k + 2.