In the definition of prequantization of representation $f\to \hat{f}$, (here $\hat{f}$ is Hermitian operator)of $C^{\infty}(M)$ on $L^2(M,L,\mu)$ where $\mu$ is Hermitian form, suppose that there exists some $(L,\mu,\Delta)$, such that $\Delta$ has the curvature $\omega$. Let given $(L,\mu)$, then why the choices of $\Delta$, should be parametrized by $\frac{H^1(M,\mathbb{R})}{H^1(M,\mathbb{Z})}$.?

This is a general fact in differential cohomology, which in degree two classifies Hermitian line bundles with connection. Differential cohomology has an exact sequence $$ 0 \to \frac{H^{k1}(M,\mathbb{R})}{H^{k1}(M,\mathbb{Z})} \to \hat H^k(M,\mathbb{Z}) \to H^k(M,\mathbb{Z}) \times_{H^k(M,\mathbb{R})} \Omega^k_{cl}(M). $$ In your case, the pair $((L,\mu),\omega)$ is an element in the group on the right hand side, and the possible prequantizations are those elements in the middle mapping to that element. EDIT: The third arrow in above sequence sends a Hermitian line bundle with connection $(L,\mu,\Delta)$ to the pair $(c_1(L),R^{\Delta})$ consisting of the first Chern class of $L$ and the curvature of $\Delta$. Two choices of $\Delta$ lead to two different elements $(L,\mu,\Delta)$ and $(L,\mu,\Delta')$ in $\hat H^2(M,\mathbb{Z})$. By your assumption that $\Delta$ and $\Delta'$ have the same curvature, the difference between the two elements lies in the kernel of the third arrow, and hence in the image of the second. 

