The Hilbert-P\'olya conjecture asserts that the non-trivial zeros of the Riemann zeta function $\zeta(s)$ correspond (in a certain canonical way) to the eigenvalues of some positive operator. R. Meyer constructed a differential operator $D_-$ acting on a function space $\H$ and showed that the eigenvalues of the adjoint of $D_-$ are exactly the nontrivial zeros of $\zeta(s)$ with multiplicity correspondence. We follow Meyer's construction with a slight modification. Specifically, we define two function spaces $\H_\cap$ and $\H_-$ on $(0,\infty)$ and characterize them via the Mellin transform. This allows us to show that $Z\H_\cap\subseteq\H_-$ where $Zf(x)=\sum_{n=1}^\infty f(nx)$. Also, the differential operator $D$ given by $Df(x)=-xf'(x)$ induces an operator $D_-$ on the quotient space $\H=\H_-/Z\H_\cap$. We show that the eigenvalues of $D_-$ on $\H$ are exactly the nontrivial zeros of $\zeta(s)$. Moreover, the geometric multiplicity of each eigenvalue is one and the algebraic multiplicity of each eigenvalue is its vanishing order as a nontrivial zero of $\zeta(s)$. We generalize our construction on the Riemann zeta function to some $L$-functions, including the Dirichlet $L$-functions and $L$-functions associated with newforms in $\mathcal S_k(\Gamma_0(M))$ with $M\ge1$ and $k$ being a positive even integer. We give spectral interpretations for these $L$-functions in a similar fashion.