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Magnetic skyrmions widely exist in a diverse range of magnetic systems, including chiral magnets with a non-centrosymmetric structure characterized by Dzyaloshinkii–Moriya interaction (DMI). In this study, we propose a generalized semi-implicit backward differentiation formula projection method, enabling the simulations of the Landau–Lifshitz (LL) equation in chiral magnets in a typical time step-size of 1 ps, markedly exceeding the limit subjected by the reported numerical methods of typically 0.1 ps. Using micromagnetics simulations, we show that the LL equation with strong DMI reveals an intriguing dynamic instability in magnetization configurations as the damping varies. Both the isolated skyrmionium and skyrmionium clusters can be consequently produced using a simple initialization strategy and a specific damping parameter. Assisted by the string method, the transition path between skyrmion and skyrmionium, along with the escape of a skyrmion from the skyrmion clusters, are then thoroughly examined. The numerical methods developed in this work not only provide a reliable paradigm to investigate the skyrmion-based textures and their transition paths, but also facilitate the understandings for magnetization dynamics in complex magnetic systems. [ABSTRACT FROM AUTHOR]