To address the difficulty in simulations of massive array microwave photonics systems and devices, a distributed cross-domain parallel simulation method is proposed in this paper. First, the pipelined parallel computation across system structural domains is achieved based on the independent transmission between the channels of a massive array microwave photonics system. Second, parallel data computing across time domains is achieved by utilizing the relative independence of pre- and post-processing times. Furthermore, a static load balancing strategy is used to assist in allocating computational resources. These two approaches are effectively combined to achieve highly efficient simulation of microwave photonics systems, which addresses the issue of long simulation times caused by large amounts of data and models. For a 64-array microwave photonics system with more than 400 models, this technique reduces the simulation time from 39 hours to 23 minutes, resulting in a simulation efficiency improvement of two orders of magnitude. This advancement holds potential for significantly reducing the development cycle of microwave photonics engineering prototypes.