In order to explore the application of handheld X-ray fluorescence spectrometer in research and protection of grottoes, based on lithofacies analysis and former geological data, we apply handheld X-ray fluorescence spectrometer to carry out high-density XRF tests on sandstone with a total thickness of 42 m from the feet to the chest of Leshan Giant Buddha in Sichuan Province at an average interval of 0.5 m and makes a curve of element content and ratio change. The research results show that the main elements such as Si, Ca, Al and Fe in the handheld XRF test results agree with the lithofacies analysis results and natural layer division results, reflecting the content changes quartz, calcite and limonite and the sericitization of debris. Element ratio can reflect the difference in weathering resistance between thick and massive rock mass. Si/(Si+Fe+Al) reflects the variation of cement content and its dissolution. (K₂O+CaO)/Al₂O₃ indicates the change of chemical weathering resistance. The decoupling of S element content with Fe and Mn indicates the development of dissolved pores, which comprehensively reflects the development of cement composition, porosity and bedding of Leshan Giant Buhhda rocks. The two high values of Cl are highly consistent with the banded stagnant water area in the chest and the unconfined water area in the feet of the Leshan Giant Buddha. Therefore, the application of handheld X-ray fluorescence spectrometer in the analysis of stone cultural relics shows the following three advantages. (1) For large and immovable stone cultural relics, handheld X-ray fluorescence spectrometer provides an efficient and non-destructive analysis method of petrochemical composition. The major elements can be in good consistence with the lithofacies analysis results of rock strata on rock mass in grottoes and the natural layer division results, which is helpful for the division of rock strata of stone cultural relics and the comparison of stone cultural relics in different regions. (2) Handheld X-ray fluorescence spectrometer can satisfy the high-resolution XRF scanning with a test interval of less than 0.1 m for the stone cultural relics in the same thick-massive rock stratum. The fluctuation of element ratio and the change of coupling relationship between elements reflect the internal difference in the weathering resistance of massive rock mass in cement composition, porosity and dissolved pore development. (3) The elemental concentration variations of Cl accurately indicate the rock strata with high water content, useful for the evaluation of water stagnation and seepage situation and the key prevention areas. It supports the comparative study of the locations and mechanisms of the stone cultural relics damages under different climatic and hydrological conditions.