This study investigates the effects of horizontal resolution and surface flux formulas on typhoon intensity and structure simulations through the case study of the Super Typhoon Haiyan (2013). Three sets of surface flux formulas in the Weather Research and Forecasting Model were tested using grid spacings of 1, 3, and 6 km. Increased resolution and more reasonable surface flux formulas can both improve typhoon intensity simulation, but their effects on storm structures differ. A combination of a decrease in momentum transfer coefficient and an increase in enthalpy transfer coefficients has greater potential to yield a stronger storm. This positive effect of more reasonable surface flux formulas can be efficiently enhanced when the grid spacing is appropriately reduced to yield an intense and contracted eyewall structure. As the resolution increases, the eyewall becomes more upright and contracts inward. The size of updraft cores in the eyewall shrinks, and the region of downdraft increases; both updraft and downdraft become more intense. As a result, the enhanced convective cores within the eyewall are driven by more intense updrafts within a rather small fraction of the spatial area. This contraction of the eyewall is associated with an upper-level warming process, which may be partly attributed to air detrained from the intense convective cores. This resolution dependence of spatial scale of updrafts is related to the model effective resolution as determined by grid spacing.