To suppress the combustion instabilities faced in the lean premixed combustion, the impacts of swirler hub configurations on combustion instabilities under elevated pressure are investigated using large eddy simulation combined with a flamelet generation manifold model. Good agreement between the numerical predictions and experimental data is achieved. The flow fields of the combustors with three distinct swirler configurations are simulated: prototype, swirler with lobes on the hub of pilot stage, and with lobes on the hub of the first main stage. Furthermore, dynamic mode decomposition (DMD) is used to extract the dynamic characteristics, and a flame transfer function (FTF) is employed to characterize the fluctuation characteristics. The results show that the prototype combustor demonstrates a coupled fluctuation between flow and heat release. Influenced by the precessing vortex core (PVC), the flame angle varies between 70° and 90° and the first DMD modes of axial velocity, temperature, and heat release rate are all at a frequency of 470 Hz. The lobes on the hub of the pilot stage suppress the formation of PVC, making the combustion very stable. The flame angle remains constant at 80°, and the gain of FTF is lower than 1. However, adding lobes to the first main stage makes the combustion extremely unstable. The flow field structure undergoes drastic changes, mimicking a “breathe” process. The flame surface is highly distorted, and flashback phenomena occur.