Background Controlling the epidemic spread and establishing the immune barrier in a short time through accurate vaccine demand prediction and optimised vaccine allocation strategy are still urgent problems to be solved under the condition of frequent virus mutations. Methods A cross-regional Susceptible-Exposed-Infected-Removed dynamic model was used for scenario simulation to systematically elaborate and compare the effects of different cross-regional vaccine allocation strategies on the future development of the epidemic in regions with different population sizes, prevention and control capabilities, and initial risk levels. Furthermore, the trajectory of the cross-regional vaccine allocation strategy, calculated using a particle swarm optimisation algorithm, was compared with the trajectories of other strategies. Results By visualising the final effect of the particle swarm optimisation vaccine allocation strategy, this study revealed the important role of prevention and control (including the level of social distancing control, the speed of tracking and isolating exposed and infected individuals, and the initial frequency of mask-wearing) in determining the allocation of vaccine resources. Most importantly, it supported the idea of prioritising control in regions with a large population and low initial risk level, which broke the general view that high initial risk needs to be given priority and proposed that outbreak risk should be firstly considered instead. Conclusions This is the first study to use a particle swarm optimisation algorithm to study the cross-regional allocation of COVID-19 vaccines. These data provide a theoretical basis for countries and regions to develop more targeted and sustainable vaccination strategies. KEY MESSAGE The innovative combination of particle swarm optimisation and cross-regional SEIR model to simulate the pandemic trajectory and predict the vaccine demand helped to speed up and stabilise the construction of the immune barrier, especially faced with new virus mutations. We proposed that priority should be given to regions where it is possible to prevent more infections rather than regions where it is at high initial risk, thus regional outbreak risk should be considered when making vaccine allocation decisions. An optimal health-oriented strategy for vaccine allocation in the COVID-19 pandemic is determined considering both pharmaceutical and non-pharmaceutical policy interventions, including speed of isolation, degree of social distancing control, and frequency of mask-wearing.