Unconventional geometric designs such as continu-ous-flow intersections, U-turns, and contraflow left-turn lanes have been proposed to reduce left-turn conflicts and improve intersection efficiency. Having a waiting area at a signalised intersection is an unconventional de-sign that is used widely in China and Japan to improve traffic capacity. Many studies have shown that waiting areas improve traffic capacity greatly, but few have con-sidered how to improve the benefits of this design from the aspect of signal optimisation. Comparing the start-up process of intersections with and without waiting areas, this work explores how this geometric design influenc-es vehicle transit time, proposes two signal optimisation strategies, and establishes a unified capacity calculation model. Taking capacity maximisation as the optimisation function, a cycle optimisation model is derived for over-saturated intersections. Finally, the relationship among waiting-area storage capacity, cycle time, and traffic ca-pacity is discussed using field survey data. The results of two cases show that optimising the signal scheme helps reduce intersection delays by 10–15%.