In this paper, it is explained that a topological invariant for 3-manifold $M$ with $b_1(M)=1$ can be constructed by applying Fukayas Morse homotopy theoretic approach for Chern--Simons perturbation theory to a local system on $M$ of rational functions associated to the free abelian covering of $M$. Our invariant takes values in Garoufalidis--Rozanskys space of Jacobi diagrams whose edges are colored by rational functions. It is expected that our invariant gives a lot of nontrivial finite type invariants of 3-manifolds.