In the present study, the supersonic flow over a three-dimensional flexible parachute system is numerically simulated using a simple "immersed boundary method" together with the weak fluid-structure coupling scheme. The parachute system employed here consists of a capsule and a canopy. The mass-spring-damper model is applied to solve the structural dynamics of the flexible parachute system. The objective of this study is to analyze the effects of aerodynamic interaction such as wake/shock interaction on the dynamics of the canopy behavior, and clarify the performance of the flexible parachute system in terms of Mach number, the ratio of a capsule to a canopy diameter, and the trailing distance between the capsule and canopy. As a result, it is found that there are two key factors for the dynamics of the parachute system: one is the unsteady change in canopy shape and the other the aerodynamic interference between the capsule wake and the canopy shock. As the trailing distance increases reasonably, the area oscillation of the canopy shape is observed. However, by reducing the canopy size in the certain smaller trailing distance case, the canopy deformation is improved. Moreover, it is found that the free stream Mach number has a big impact on the canopy behavior in the smaller Mach number case, where the canopy undergoes smaller deformation, leading to a larger drag coefficient.