Complex systems widely exist in nature and human society. There are complex interactions between system elements in a complex system, and systems show complex features at the macro level, such as emergence, self-organization, uncertainty, and dynamics. These complex features make it difficult to understand the internal operation mechanism of complex systems. Networked modeling of complex systems is a favorable means of understanding complex systems. It not only represents complex interactions but also reflects essential attributes of complex systems. This paper summarizes the research progress of complex systems modeling and analysis from the perspective of network science, including networked modeling, vital node analysis, network invulnerability analysis, network disintegration analysis, resilience analysis, complex network link prediction, and the attacker-defender game in complex networks. In addition, this paper presents some points of view on the trend and focus of future research on network analysis of complex systems.