The study of interconnection networks is important because the overall performance of a distributed system is often critically hinged on the effectiveness of its interconnection network. In the mean time, the heterogeneity is one of the most important factors of such systems. This paper addresses the problem of interconnection networks performance modeling of large-scale distributed systems with emphases on heterogeneous multi-cluster computing systems. So, we present an analytical model to predict message latency in multi-cluster systems in the presence of cluster size heterogeneity. The model is validated through comprehensive simulation, which demonstrates that the proposed model exhibits a good degree of accuracy for various system organizations and under different working conditions.