Malware is pervasive in networks, and poses a critical threat to network security. However, we have very limited understanding of malware behavior in networks to date. In this paper, we investigate how malware propagate in networks from a global perspective. We formulate the problem, and establish a rigorous two layer epidemic model for malware propagation from network to network. Based on the proposed model, our analysis indicates that the distribution of a given malware follows exponential distribution, power law distribution with a short exponential
tail, and power law distribution at its early, late and final stages, respectively. Extensive experiments have been performed through two real-world global scale malware data sets, and the results confirm our theoretical findings.