The oil-free twin screw compressors have obtained increasing attention in the field of boil off gas (BOG) recovery since they effectively reduce the power consumption and have higher reliability when recovering and boosting BOG. However, the thermal deformation of compressor under cryogenic operating conditions will lead to the change of clearance. The unidirectional thermal-fluid-solid coupling method is proposed in this paper to solve the problem and analyze the thermal deformation of compressor and the changes of each clearance caused by the deformation at different meshing angles in a meshing cycle. It is shown in the results that the deformation of twin screw compressor at low temperatures is a kind of cold shrinkage deformation. The combined effect of the deformation of various components has a significant influence on each clearance. Furthermore, it is reasonable to set the tooth tip clearance of the male rotor, suction end clearance and meshing gap as 0.3 mm, 1 mm and 0.3 mm respectively, which do not cause dangerous working conditions. Inappropriate clearance values lead to friction between parts in the local area. The simulated result of the dangerous friction area in twin screw compressor shows good agreement with the friction area in the compressor test. According to the simulation and test results, the tooth tip clearance of the female rotor is modified to 0.35 mm, and the discharge end clearance is adjusted to 0.1 mm. The results show that the modified compressor can working reliably. This study provides guidance for the design and processing of oil-free twin screw compressors employed in the situation of BOG recovery.