Previous research regarding PhD students’ well-being (PhD-WB) has lacked a comprehensive and systemic analysis. This research engages with a systems approach to examine the multiple variables, including feedback mechanisms, which influence PhD-WB over time. The model was developed using a structural analysis method (Cross-impact analysis MICMAC) that informed a causal loop diagram (CLD). The aim was to understand what promotes (drivers) and inhibits (barriers) PhD students’ well-being. The results show that PhD students’ well-being reflects an interplay between university, financial support, students’ mental and physical health, and family/friends. However, the analysis shows that the role of the drivers is dynamic, and they can become barriers in certain circumstances. This insight validates the application of systems thinking to illustrate the complexity of PhD students’ well-being.