Mathematical optimization is now widely regarded as an indispensable modeling and solution tool for the design of wireless communications systems. While optimization has played a significant role in the revolutionary progress in wireless communication and networking technologies from 1G to 5G and onto the future 6G, the innovations in wireless technologies have also substantially transformed the nature of the underlying mathematical optimization problems upon which the system designs are based and have sparked significant innovations in the development of methodologies to understand, to analyze, and to solve those problems. In this paper, we provide a comprehensive survey of recent advances in mathematical optimization theory and algorithms for wireless communication system design. We begin by illustrating common features of mathematical optimization problems arising in wireless communication system design. We discuss various scenarios and use cases and their associated mathematical structures from an optimization perspective. We then provide an overview of recently developed optimization techniques in areas ranging from nonconvex optimization, global optimization, and integer programming, to distributed optimization and learning-based optimization. The key to successful solution of mathematical optimization problems is in carefully choosing or developing suitable algorithms (or neural network architectures) that can exploit the underlying problem structure. We conclude the paper by identifying several open research challenges and outlining future research directions.