The harmonic index of a graph $G$ is defined as the sum of weights $\frac{2}{d(u)+d(v)}$ of all edges $uv$ of $G$, where $d(u)$ and $d(v)$ are the degrees of the vertices $u$ and $v$ in $G$, respectively. In this paper, we determine the graph with minimum harmonic index among all unicyclic graphs with a perfect matching. Moreover, the graph with minimum harmonic index among all unicyclic graphs with a given matching number is also determined.