Layered molybdenum trioxide (α-MoO3) has been widely investigated as a promising Li battery cathode material. However, its low conductivity and irreversible structure change during charge–discharge process leads to its poor electrochemical performance. Although several methods have been reported to increase its conductivity, the issue of structure degradation still hinders its practical application. Here, a Na+ pre-intercalation strategy was proposed. The Na ions were successfully pre-intercalated into MoO3 nanobelts via a facile method, and the intercalation amount can be well controlled. Compared to pristine MoO3, the Na+ pre-intercalated nanobelts exhibit significant improvement in cycling stability as well as rate capability. Through in-situ XRD analyses combined with the electrochemical tests, it is demonstrated that the Na ions between the Mo–O interlayers effectively inhibit the irreversible phase transition and stabilize the layered structure. The inhibiting effect and the proposed Na+ pre-intercalation strategy are fundamentally important to further promote the development of molybdenum based or other layered electrode materials.