In this paper, we numerically investigate the length spectra and the low-lying eigenvalue spectra of the Laplace-Beltrami operator for a large number of small compact(closed) hyperbolic (CH) 3-manifolds. The first non-zero eigenvalues have been successfully computed using the periodic orbit sum method, which are compared with various geometric quantities such as volume, diameter and length of the shortest periodic geodesic of the manifolds. The deviation of low-lying eigenvalue spectra of manifolds converging to a cusped hyperbolic manifold from the asymptotic distribution has been measured by ζ− function and spectral distance.