Summary: This paper presents a method to compute the quasi-conformal parameterization (QCMC) for a multiply-connected 2D domain or surface. QCMC computes a quasi-conformal map from a multiply-connected domain \(S\) onto a punctured disk \(D_S\) associated with a given Beltrami differential. The Beltrami differential, which measures the conformality distortion, is a complex-valued function \(\mu :S\to \mathbb {C}\) with supremum norm strictly less than 1. Every Beltrami differential gives a conformal structure of \(S\). Hence, the conformal module of \(D_S\), which are the radii and centers of the inner circles, can be fully determined by \(\mu\), up to a Möbius transformation. In this paper, we propose an iterative algorithm to simultaneously search for the conformal module and the optimal quasi-conformal parameterization. The key idea is to minimize the Beltrami energy with the conformal module of the parameter domain incorporated. The optimal solution is our desired quasi-conformal parameterization onto a punctured disk. The parameterization of the multiply-connected domain simplifies numerical computations and has important applications in various fields, such as in computer graphics and vision. Experiments have been carried out on synthetic data together with real multiply-connected Riemann surfaces. Results show that our proposed method can efficiently compute quasi-conformal parameterizations of multiply-connected domains and outperforms other state-of-the-art algorithms. Applications of the proposed parameterization technique have also been explored.