Response surface methodology was used to estimate the optimum extraction parameters, for which the total phenolic content and total flavonoid content of Avicennia officinalis L. extract were the highest. Based on the 3D surface plots and regression analysis of the independent variables, the optimal conditions for the ultrasound-assisted extraction were as follows: methanol content, 55.27%; liquid-to-solid ratio, 14:1 (mL/g, v/w); temperature, 48.8 °C, and time, 9.66 min. Optimal extraction conditions were applied to validate the quantification. The bioactive compounds from the Avicennia officinalis L. extract were identified through ultra-fast liquid chromatography coupled to diode array detector for the first time. These methods were applied to quantify phenolic acids and flavonoids from A. officinalis extracts collected at six different locations in Vietnam. The results showed that the concentrations of these compounds varied from 0.319 ± 0.022 to 3.524 ± 0.125 mg/g in the methanol extract. The result showed that cinnamic acid is the major compound in A. officinalis collected in Vietnam. In the present study, an optimized ultrasound-assisted extraction was first designed to improve the content of phenolic acids and flavonoid compounds from A. officinalis. Additionally, the bioactive compounds from the A. officinalis extract were identified through UFLC-DAD for the first time.