In the experiments of actively triggering plasma disruption by massive gas injection, the externally applied resonant magnetic perturbation has been used to mitigate the hazard of runaway electron (RE). Motivated by the experiment of multimode coupling to suppress REs on J-TEXT, some typical simulation cases with NIMROD code are carried out to explore the influential mechanism of different relative phases between m/n = 2/1 and m/n = 3/1 magnetic islands on the confinement of REs. Results show that the RE confinement is drastically affected by the relative phase between 2/1 and 3/1 magnetic islands. When the “O point” phase of 2/1 and 3/1 magnetic islands are toroidal 330°, REs can be effectively lost. The fitting curve of the remaining ratio of REs vs. the relative toroidal phase is predicted to approximate a sine-like function dependence. Further studies on the relationship between the magnetic topological structure and the RE loss indicate that the phase difference between coexisting 2/1 and 3/1 islands can cause different degrees of stochasticity and RE loss.