In the past decades, many methods for computing conformal mesh parameterizations have been developed in response to demand of numerous applications in the field of geometry processing. Spectral conformal parameterization (SCP) (Mullen et al. in Proceedings
of the symposium on geometry processing, SGP ’08. Eurographics Association, Aire-la-Ville, Switzerland, pp 1487–1494, 2008) is one of these methods used to compute a quality conformal parameterization based on the spectral techniques. SCP focuses on a generalized eigenvalue problem (GEP) $L_{C} \bf{f} = \lambda B \bf{f}$ whose eigenvector(s) associated with the smallest positive eigenvalue(s) provide the conformal parameterization result. This paper is devoted to studying a novel eigensolver for this GEP. Based on structures of the matrix pair $(L_{C}, B)$, we show that this GEP can be transformed into a small-scale compressed and deflated standard eigenvalue problem with a symmetric positive definite skew-Hamiltonian operator. We then propose a symmetric skew-Hamiltonian isotropic Lanczos algorithm (SHILA) to solve the reduced problem. Numerical experiments show that our compressed deflating technique can exclude the impact of convergence from the kernel of $L_{C}$ and transform the original problem to a more robust system. The novel SHILA method can effectively avoid the disturbance of duplicate eigenvalues. As a result, based on the spectral model of SCP, our numerical eigensolver can compute the conformal parameterization accurately and efficiently.