We construct an obstruction to the existence of embeddings of a homology 3-sphere into a homology S 3 × S 1 under some cohomological condition. The obstruction are defined as an element in the filtered version of the instanton Floer cohomology due to [6]. We make use of the Z-fold covering space of homology S 3 × S 1 and the instantons on it.We will use the following assumption on Y in our main theorem(Theorem 2.4).Assumption 2.2. All SU (2) flat connections on Y are non-degenerate, i.e. the first cohomology group of the next twisted de Rham complex:Example 2.3. All flat connections on the Brieskorn homology 3-sphere Σ(p, q, r) are non-degenerate.([5])Under Assumption 2.2, l Y is finite ([14]). In this paper without the use of Assumption 2.2, we will introduce the following invariants:• Q i X ∈ R ≥0 ∪ {∞} for i ∈ N and X in Definition 4.6 (When X is homotopy equivalent to S 3 × S 1 , Q i X = ∞ for all i ∈ N). Our main theorem is: Theorem 2.4. Under Assumption 2.2, if there exists an embedding f of Y into X with f * [Y ] = 1 ∈ H 3 (X, Z) then [θ r ] vanishes for any r ∈ [0, min{Q 2lY +3 X , 1}]∩ (R \ cs Y ( R(Y )) ∪ {∞})