The effect of inner core asymmetries on tropical cyclone (TC) intensity is investigated via a comparative study using a triply nested 3D tropical cyclone model (TCM3) and its axisymmetric version. Both 3D and axisymmetric models have identical numerics and physics; both are integrated from the same initial conditions on an f-plane with no environmental flow. The results show that the presence of asymmetric component in the 3-D experiment reduces TC intensity in the mature stage. Angular momentum, radial wind, PV and equivalent potential temperature budgets for the two simulations are evaluated, respectively, with the focus on the influence of inner core asymmetry on TC intensity through changing the symmetric circulation. A key factor that determines the equilibrium TC intensity is the entropy deficit at the air-sea interface under the eyewall. In the symmetric TC, an annular tower of high PV with low PV within the eyewall is formed due to the convective heating in the eyewall. The tilting of the eyewall is consistent with the theory of slantwise neutral convection. Downdrafts under the tilted eyewall dry and cool the subcloud-layer, increasing entropy deficit at the air-sea interface under the eyewall. For the 3D TC, the reverse of the radial PV gradient in the inner core region sets up dynamical instability, causing PV rearrangement. The PV rearrangement is most significant at the upper troposphere due to low inertial stability, resulting in a less tilted eyewall, which is unfavorable for the formation of strong downdrafts underneath. As a result, the entropy deficit at the air-sea interface under the eyewall is smaller compared to the axisymmetric TC, thus the final intensity is reduced. Dynamically, the low-level lateral eddy mixing by resolved eddies (vortex Rossby waves) is dominated in 3D run while the parameterized lateral diffusion is dominated in axisymmtric run near the radius of maximum wind. The total mixing in 3D run is larger than that in axisymmetric run, explaining some extra dissipation for the symmetric cyclone from the resolved eddies in the eyewall.