Interaction between the acidic motif (AM) of protein kinase WNK4 and the Kelch domain of KLHL3 are involved in the pathogenesis of pseudohypoaldosteronism type II, a hereditary form of hypertension. This interaction is disrupted by some disease-causing mutations in either WNK4 or KLHL3, or by angiotensin II- and insulin-induced phosphorylation of KLHL3 at serine 433, which is also a site frequently mutated in patients. However, the mechanism by which this phosphorylation disrupts the interaction is unclear. In this study, we approached this problem using molecular dynamics simulation with structural, dynamical and energetic analyses. Results from independent simulations indicate that when S433 was phosphorylated, the electrostatic potential became more negative in the AM binding site of KLHL3 and therefore was unfavorable for binding with the negatively charged AM. In addition, the intermolecular hydrogen bond network that kept the AM stable in the binding site of KLHL3 was disrupted, and the forces for the hydrophobic interactions between the AM of WNK4 and KLHL3 were also reduced. As a result, the weakened interactions were no longer capable of holding the AM of WNK4 at its binding site in KLHL3. In conclusion, phosphorylation of KLHL3 at S433 disrupts the hydrogen bonds, hydrophobic and electrostatic interactions between the Kelch domain of KLHL3 and the AM of WNK4. This study provides a key molecular understanding of the KLHL3-mediated regulation of WNK4, which is an integrative regulator of electrolyte homeostasis and blood pressure regulation in the kidney. Significances Statement: WNK4 is an integrative regulator of electrolyte homeostasis, which is important in the blood pressure regulation by the kidney. Interaction between WNK4 and KLHL3 is a key physiological process that is impaired in a hereditary form of hypertension. This study provides substantial new insights into the role of phosphorylation of KLHL3 in regulating the interaction with WNK4, and therefore advances our understanding of molecular pathogenesis of hypertension and the mechanism of blood pressure regulation.