The pilot stage plays a crucial role in central-staged combustion technology. This study aimed to investigate the impact of the jet-type pilot stage on the flame structure and combustion instability in a novel strong coupled centrally staged swirl gas turbine combustor, using both experiments and large eddy simulations (LES). Nonlinear dynamic analyses of dynamic pressure, including phase and recurrence plots, were performed alongside a proper orthogonal decomposition of the dynamic flame structures. It is indicated that a richer pilot stage worsens the instability of the centrally staged combustion system. An increase in the equivalence ratio of the pilot stage leads to enhanced non-premixed combustion and a downstream shift in the heat release region. The transition results in the shift of flame shape from an attached V-shaped flame to an intermittent lifting U-shaped flame. The flame surface statistics from LES results including the strain rate and progress variable gradient of lean and rich pilot conditions were compared. Under richer pilot conditions, the lifting U-shaped flame demonstrates increased sensitivity to flow field fluctuations, intensifying vortex–flame interactions. This interaction causes the large-scale flame surface stretching and even extinction of the pilot stage flame, exacerbating combustion instability observed in this study. These insights offer a deeper understanding of the impact of the jet-type pilot stage on the novel multi-staged central combustion systems.