Objective To establish a HPLC method for in vivo determination of gallic acid (GA) and protocatechuic acid (PA) in rat plasma, and to study the effect of Sandalwood on the pharmacokinetics of GA and PA. Methods SD rats were given the water extracts of Choerospondiatis fruit or Choerospondiatis fruit and Sandalwood. The pharmacokinetic parameters of GA and PA were calculated by DAS2.0 software at different time points after an oral ration of the above extracts. Results The pharmacokinetic parameters after oral administration of Choerospondiatis fruit extract were as follows:GA: Cmax:(0.112±0.008) mg·L-1, CL/F: (0.132±0.016) L·min-1·kg-1, t1/2β: (69.3±0) min, Tmax: (45.0±0) min; PA: Cmax: (0.550±0.028) mg·L-1, Tmax: (52.0±0) min, t1/2β: (60.7±1.1) min; CL/F: (0.078±0.011) L·min-1·kg-1. The pharmacokinetic parameters after oral ration of Choerospondiatis fruit-Sandalwood extract were as follows: GA: Cmax: (0.187±0.010) mg·L-1, CL/F: (0.094±0.017) L·min-1·kg-1, t1/2β:(69.3±3.3) min, Tmax: (30.0±0) min; PA: Cmax: (1.080±0.066) mg·L-1, Tmax: (45.0±0) min, t1/2β: (69.3±0.2) min, CL/F:(0.011±0.001) L·min-1·kg-1. Conclusion Oral ration of Choerospondiatis fruit-Sandalwood extract results in earlier plasma peaks of PA and GA, lower clearance rate, and longer half life, indicating Sandalwood can promote the absorption of phenolic compounds in Choerospondiatis fruit.