Hetian jade pebbles are secondary ores of Hetian jade that have been washed, carried and deposited by rivers for a long time, and are popular among consumers for their unique epidermis colors. For some time, the rising price of Hetian jade pebbles has led to the emergence of many artificially produced counterfeits on the market. Identifying Hetian jade pebbles and counterfeits has become a difficult problem for consumers, practitioners and even identification laboratories. In this paper, a representative group of Xinjiang Hetian jade pebbles from reliable sources were selected for the study, and the samples were confirmed as Hetian jade pebbles based on their morphological and epidermis color distribution characteristics. The secondary minerals of the representative Hetian jade pebbles samples were investigated by gemological microscopy, Raman spectroscopy, infrared spectroscopy, X-ray diffraction spectroscopy, and UV-Vis diffuse reflectance spectroscopy. According to gemological microscopy, in addition to the red to-yellow epidermis and brownish-black dendritic mineral aggregates, there are parallel-arranged flaky mineral aggregates in the fissures, fibrous minerals and minerals with complete cleavage planes and uneven film-like distribution of secondary minerals in the pits of the epidermis of Hetian jade pebbles. Raman spectroscopy results show that the main mineral on the epidermis of Hetian jade pebbles is tremolite, as is in the interior. The fluorescence intensity of the Raman spectrum of the Hetian jade pebbles is related to the degree of weathering in the tested area. The fluorescence of the strong weathering products not only obscures the Raman peaks of the secondary minerals, but also weakens the minor peaks of the primary mineral tremolite. Infrared spectroscopy and X-ray powder crystal diffraction tests show that the parallel arranged flaky mineral aggregates in the fissures of the epidermis, the fibrous minerals and the minerals with sparkling eminent cleavage planes and the unevenly distributed film-like secondary minerals in the pits of the epidermis are all clinochlore. The first derivative of the UV-vis diffuse reflectance spectra of the red and yellow epidermis have 430 and 520～541 nm peaks, and some samples have spectral peaks near 575 nm, indicating that the chromogenic minerals are goethite and hematite. The spectroscopic study of the epidermal secondary minerals of the Hetian jade pebbles shows that they have undergone a series of epigenetic geological actions under the long-term effect of geological forces such as atmosphere and water, forming secondary minerals such as clinochlore and goethite, which provides a scientific basis for the study of the identification of Hetian jade pebbles and the distinction from counterfeits.