Abstract: Using long-term Whole Atmosphere Community Climate Model version 5 (WACCM5) simulations initialized with the climatology around the year 2000, we studied the anomalous distribution of planetary wave and gravity wave fluxes during distinct phases of the boreal stratospheric polar vortex (BSPV) and Quasi-Biennial Oscillation (QBO). The contributions of these two types of waves to Brewer–Dobson circulation (BDC) anomalies were further analyzed. The results revealed that under four distinct phases, the northern hemisphere BDC is primarily governed by planetary waves, whereas gravity waves counteract approximately half of the planetary wave influence on the BDC in the upper stratosphere. The QBO regulates the position of the anomaly center within the BDC’s descending branch in the northern hemisphere. In particular, during the westerly phase of the QBO (WQBO), the center of this anomalous descending branch is located in the upper stratosphere, whereas during the easterly phase of the QBO (EQBO), it is located in the lower stratosphere. Southern hemisphere BDC anomalies are regulated more by QBO activity: during the WQBO, it shows synchronous changes with the BDC anomaly in the northern hemisphere, whereas during the EQBO, it exhibits an antiphase relationship with the BDC anomaly in the northern hemisphere. Mesospheric circulation anomalies are predominantly driven by gravity wave activity. The circulation weakens during a weak BSPV and strengthens during a strong BSPV. Additionally, the descending branch anomaly of the northern hemisphere circulation is more pronounced during the WQBO, whereas the ascending branch anomaly of the southern hemisphere circulation is more significant during the EQBO.