Ferromagnetism and exotic topological structures in SrRuO$_3$ (SRO) induce sign-changing anomalous Hall effect (AHE). Recently, hump structures have been reported in the Hall resistivity of SRO thin films, especially in the ultra-thin regime. We investigate the AHE and hump structure in the Hall resistivity of SRO ultra-thin films with an SrTiO$_3$ (STO) capping layer and ionic liquid gating. STO capping results in sign changes in the AHE and modulation of the hump structure. In particular, the hump structure in the Hall resistivity is strongly modulated and even vanishes in STO-capped 4 unit cell (uc) films. In addition, the conductivity of STO-capped SRO ultra-thin films is greatly enhanced with restored ferromagnetism. We also performed ionic liquid gating to modulate the electric field at SRO/STO interface. Drastic changes in the AHE and hump structure are observed with different gate voltages. Our study shows that the hump structure as well as the AHE can be controlled by tuning inversion symmetry and the electric field at the interface.