We first state two big results, namely Kneser-Milnor prime decomposition of $3$-manifolds and Poincaré conjecture (proven by Perelman).
After that we prove the following:
Each closed orientable $3$-manifold $M$ other than $\Bbb S^3$ has a prime decomposition $$M\cong \left(\displaystyle\sharp_{i=1}^m M_i\right)\sharp\left(\displaystyle\sharp_{j=1}^n N_j\right)\sharp\left(\displaystyle\sharp^k \Bbb S^1\times \Bbb S^2\right),$$
where each $M_i$ is aspherical (equivalently, $\Bbb R^3$ covers each $M_i$ by Thurston's geometrization theorem); each $N_j$ has non-trivial finite fundamental group, i.e., each $N_j$ is covered by $\Bbb S^3$.
Moreover, such a decomposition is unique up to orders and homeomorphisms.