The Ponciri fructus immaturus (Poncirus trifoliata Rafinesque) has been used in oriental medicine for uterine contraction, stomachache, abdominal distension and cardiovascular diseases. Two main compounds, poncirin and naringin were successfully analyzed by high performance liquid chromatography (HPLC) and carried out method validation according to ICH guideline. A successful resolution and retention times were obtained with a $C_{18}$ reversed phase column, at an $1m{ell}min^{-1}$ flow rate, with a gradient elution of a mixture of methanol, water and acetonitrile. Poncirin and naringin showed good linearity ($R^2$ > 0.999) in relatively wide concentration ranged. The recovery of each compound was 95.81 ~ 101.48% with R.S.D. values less than 1.0%. The application of ultrasound-assisted extraction was shown to be more efficient in extracting poncirin and naringin from Ponciri fructus immaturus. The predicted optimal poncirin and naringin yield were poncirin 2.15%, naringin 1.65% under an extraction temperature of $40^{circ}C$, an extraction time of 10 min in a solvent of 70% methanol.