(1) Background: A combination of radiofrequency (RF) volumetric heating and convection cooling has been proposed to realize plaque ablation while protecting the endothelial layer. However, the depth of the plaque and the thickness of the endothelial layer vary in different atherosclerotic lesions. Current techniques cannot be used to achieve penetrating heating for atherosclerosis with two targets (the specified protection depth and the ablation depth). (2) Methods: A tissue-mimicking phantom heating experiment simulating atherosclerotic plaque ablation was conducted to investigate the effects of the control parameters, the target temperature (Ttarget), the cooling water temperature (Tf), and the cooling water velocity (Vf). To further quantitatively analyze and evaluate the ablation depth and the protection depth of the control parameters, a three-dimensional model was established. In addition, a conformal penetrating heating strategy was proposed based on the numerical results. (3) Results: It was found that Ttarget and Tf were factors that regulated the ablation results, and the temperatures of the plaques varied linearly with Ttarget or Tf. The simulation results showed that the ablation depth increased with the Ttarget while the protection depth decreased correspondently. This relationship reversed with the Tf. When the two parameters Ttarget and Tf were controlled together, the ablation depth was 0.47 mm–1.43 mm and the protection depth was 0 mm–0.26 mm within 2 minutes of heating. (4) Conclusions: With the proposed control algorithm, the requirements of both the ablation depth and the endothelium protection depth can be met for most plaques through the simultaneous control of Ttarget and Tf.