Biodegradable magnesium alloy stents (MAS) are a promising solution for long-term adverse events caused by interactions between vessels and permanent stent platforms of drug eluting stents. However, the existing MAS showed severe lumen loss after a few months: too short degradation time may be the main reason for this drawback. In this study, a new design concept of MAS was proposed and a shape optimization method with finite element analysis was applied on two-dimensional (2D) stent models considering four different magnesium alloys: AZ80, AZ31, ZM21, and WE43. A morphing procedure was utilized to facilitate the optimization. Two experiments were carried out for a preliminary validation of the 2D models with good results. The optimized designs were compared to an existing MAS by means of three-dimensional finite element analysis. The results showed that the final optimized design with alloy WE43, compared to the existing MAS, has an increased strut width by approximately 48%, improved safety properties (decreased the maximum principal stress after recoil with tissue by 29%, and decreased the maximum principal strain during expansion by 14%) and improved scaffolding ability (increased by 24%). Accordingly, the degradation time can be expected to extend. The used methodology provides a convenient and practical way to develop novel MAS designs.