To investigate the landing performance of airbag cushion systems on the discrete lunar soil, this study proposes a novel modeling approach that couples multi-physics fields, including the flexible multibody systems (FMBS), the granular systems, and the gas effects. In this model, the GPU parallelism technique is utilized to address challenges arising from the large number of particles and complex contact detection involving large deformation and overall motions, and an efficient contact implementation between finite elements and particles is introduced. Additionally, contact modeling between airbags is realized using master–slave techniques. Then, a modified conventional serial staggered procedure is employed to couple flexible multibody dynamics (FMBD) and discrete element method (DEM) modules. Finally, a series of numerical examples is presented to validate the proposed dynamic model. The validated model successfully simulates the interaction between landing airbags and lunar soil. Subsequent parametric analysis contributes to the design optimization of the landing system. Moreover, discussions regarding computational efficiency illustrate that the proposed CPU–GPU-based FMBD-DEM is advantageous in engineering scenarios involving flexible components and large-scale granular systems.