Geothermal energy has significant potential to reduce fossil fuel consumptions and environmental impacts. To improve energy conversion efficiency of geothermal energy systems, numerous systems designs have been proposed and their optimization sought. At this point, it is worth reviewing current developed geothermal energy systems because understanding configurations and principles of basic and state-of-the-art technologies is important for developing advanced energy systems. A comprehensive review of the geothermal energy systems is carried out from the perspective of systems analysis, design, and optimization. Results illustrate that limited sets of parameters have been considered in most studies on design and optimization, though these studies provide great insight into specific designs. However, all influential factors have to be fully considered for practical applications. This study identifies and organizes influential factors for geothermal energy systems. In addition, critical analyses of studies on systems design and optimization are performed to determine limitations of current studies. As polygeneration systems produce various energy products (electricity, heat, and/or cooling), it might play key roles to maximize utilization of geothermal energy. Especially, polygeneration systems with binary technology, which can effectively produce electricity from moderate temperature geothermal resources, have significant potentials to enhance the overall performance. In this regard, the energy production strategy and technology selection are of significant importance to meet electric, heating, and cooling loads efficiently. To fill the knowledge gaps and to maximize geothermal energy utilization, this review proposes state-of-the-art multi-scale modeling and optimization framework.