With the increasing number of ion qubits and improving performance of sophisticated quantum algorithms, more and more scalable complex ion trap electrodes have been developed and integrated. Nonlinear ion shuttling operations at the junction are more frequently used, such as in the areas of separation, merging, and exchanging. Several studies have been conducted to optimize the geometries of the radio-frequency (RF) electrodes to generate ideal trapping electric fields with a lower junction barrier and an even ion height of the RF saddle points. However, this iteration is time-consuming and commonly accompanied by complicated and sharp electrode geometry. Therefore, high-accuracy fabrication process and high electric breakdown voltage are essential. In the current work, an effective method was proposed to reduce the junction's pseudo-potential barrier and ion height variation by setting several individual RF electrodes and adjusting each RF voltage amplitude without changing the geometry of the electrode structure. The simulation results show that this method shows the same effect on engineering the trapping potential and reducing the potential barrier, but requires fewer parameters and optimization time. By combining this method with the geometrical shape-optimizing, the pseudo-potential barrier and the ion height variation near the junction can be further reduced. In addition, the geometry of the electrodes can be simplified to relax the fabrication precision and keep the ability to engineer the trapping electric field in real-time even after the fabrication of the electrodes, which provides a potential all-electric degree of freedom for the design and control of the two-dimensional ion crystals and investigation of their phase transition.