Agarwood is the dark resinous and aromatic wood harvested from Aquilaria trees belong to Thymelaeaceae. It has great value as a raw material for perfume and traditional Chinese medicine. Agarwood is wildly accepted from natural forests and plantations. The former has more highly valued. This paper focused on distinguishing the wild agarwood from sustainably produced cultivated agarwood using high performance liquid chromatography (HPLC) combined with statistical analysis. 10 cultivated and 30 wild agarwood samples were used to respectively establish agarwood HPLC characteristic chromatograms by multivariate analysis. By the retention time and peak area analyses of two types of agarwood, characteristic chromatograms and characteristic peaks (i.e., 10 characteristic peaks of cultivated agarwood (CPC1-10) and 9 characteristic peaks of wild ones (CPW1-9)) were established. The principal component analysis (PCA) and sample validation further verified the accuracy and feasibility of the characteristic chromatograms and characteristic peaks. The difference of the HPLC characteristic chromatograms of cultivated and wild agarwood helps to differentiate these two types and provides a reliable method for ensuring wild agarwood used for high value products.