With the rapid development of shale gas resources in China, there is an increasing demand for large and multiple column compressors. However, this development has brought to light the issue of torsional vibration in compressor crankshaft systems, particularly under variable loads and multiple working conditions. In order to reduce the torsional vibration of the compressor crankshaft and ensure the safe and stable operation of the compressor unit, this study proposes a method for calculating and suppressing torsional vibration in the crankshaft system of a shale gas compressor, which takes into account the flexibility effect of various parts and considers multiple working conditions. The analysis focused on the rigid-flexible coupling torsional vibration characteristics of the crankshaft system under multiple working conditions, considering the flexible deformation of the main bearing, connecting rod, and crankshaft. The study successfully determined the torsional vibration response of the crankshaft system under seven typical working conditions. Furthermore, for the worst conditions, a detailed analysis of the vibration response of the crankshaft system was conducted and carried out a study on suppressing crankshaft torsional vibration through response surface optimization design. The study findings indicate that the compressor system exhibits low-frequency vibrations during operation. The maximum torsional angular deformation at the crank pin of the fourth column is measured to be 0.052°. Following structural optimization, the relative torsional angular deformation of the crank pin is reduced by 25.61% under the worst operating conditions. Moreover, the peak angular velocity of the center of mass is reduced by 22.17%. These results demonstrate a significant suppression effect on torsional vibrations in the compressor crankshaft system, leading to improved working safety.