In the fields of cultural relic protection, the diseases on the surface of stone relics affect the conservation and artistic quality of relics. The cleaning methods must be investigated to solve the problem. Compared with the conventional cleaning methods (e.g., chemistry cleaning and sand blasting), laser cleaning is characterized by cleaning objects without damage, strong decontaminaton ability, precise removal, avoiding pollution environments. In the paper, laser cleaning is used for removing the contaminations on the surface of stone relics. Firstly, laser induced damage experiments are carried out. The results show that the laser induced damage threshold of the sandstones is about 73.5 mJ for 1064 nm laser after 10 laser pulses. Meanwhile, the finite element analysis software is used to calculate the temperature and the stress of the sandstones under the laser irradiation. The simulated results are consistent with the experimental ones. The optimal methods and laser parameters are achieved in the laboratory experiments for removal of the ink contamination. The experiments of Bishui temple located in Sichuan province indicate that the laser cleaning is safe and effective for the removal of black smudges.