The Mayer-Vietoris theorem is known for its wide applications, especially in determining homology. In fact, this theorem provides us with a long exact sequence, where the underlying homology groups fit in. However, this theorem does not provide an explicit way to compute homology. In this paper we prove an ``effective" version of the Mayer-Vietoris theorem using discrete Morse theory. Suppose, we have a Mayer-Vietoris type setup, i.e., let $X$ be a simplicial complex and $A$ and $B$ be two subcomplexes of $X$, such that $A \cup B=X$. Moreover, let $\mathcal{W}_A$, $\mathcal{W}_{B}$ and $\mathcal{W}_{A \cap B}$ be gradient vector fields on $A$, $B$ and $A \cap B$ respectively (which need not be ``coherent", i.e., they do not need to coincide on their intersection). Then, the main theorem of our paper provides an explicit way to compute the homology groups of $X$, using the combinatorial information regarding the trajectories of the aforementioned gradient vector fields, we do not even need to know the individual homology groups $H_{*}(A)$, $H_{*}(B)$ and $H_{*}(A \cap B)$. In principle, the homology of $X$ can always be computed explicitly using our theorem irrespective of the choice of the gradient vector fields. Further, if we choose the subcomplexes $A$ and $B$ wisely so that each of $A$, $B$ and $A \cap B$ admits an efficient gradient vector field, then the computation of the homology groups is considerably reduced.