The low-emission technology of gas turbine combustors is currently an active area of research. In light-duty lean-premixed combustors, achieving rapid and uniform fuel mixing presents significant challenges. Additionally, combustion instability issues are also likely to occur. To address these challenges, large eddy simulation and the flamelet generation manifold combustion model are used to predict the velocity field, fuel distribution, vortex structure, flame structure, and flame liftoff phenomenon in a low-emission tower-type coaxial-staged combustor. The results indicate that variations in the position of the fuel holes in the second main stage result in two types of fuel injection modes: coupling and decoupling. These variations do not significantly influence the velocity and vortex structure in a non-reacting flow. The dominant frequency of the non-reacting flow field in the combustor is 810 Hz. The position of the precessing vortex core affects the distribution of fuel. Furthermore, the uniformity of fuel distribution at the outlet of the second main stage is notably affected by different fuel injection modes. The spatial distribution of fuel is more uniform. In the reacting flow, compared to the decoupling mode, the fuel expansion angle decreases by 4.5° under the coupling mode, and the heat release at the flame front is more intense. Additionally, it is found that fuel injection modes significantly influence the dynamic characteristics at the flame root. Better flame stability is observed under the decoupling mode, while flame liftoff phenomena occur under the coupling mode. The lifted flame root shifts downstream by 12.3 mm.