The aim of this study is to explore the long-term influence of tunnelling on the adjacent pile foundation under cyclic change of groundwater level. A three-dimensional centrifugal model test is conducted to investigate the long-term effect of tunneling on a pile group while the groundwater level changes cyclically. The long-term surface settlement, additional pile head subsidence, additional bending moment and additional axial force of pile are examined. The results show that the long-term surface subsidence is influenced more significantly by the cyclically varying groundwater level induced, particularly, by precipitation. The long-term surface settlement increases with the number of cycle, showing an attenuation-type deformation; it is not convergent after three times of water level fluctuation cycle. The long-term additional subsidence of pile foundation is remarkable, accounting for more than 50% of the total settlement. Generally, the values of the long-term additional axial forces of front pile and rear pile are positive; if the total axial force increases, it can adversely influence the existing bearing pile. The inflection point and the maximum of the additional axial force are different. The inflection point number of bending moment of the front pile and rear pile decreases after three times of groundwater level cycles. However, the maximum additional bending moments of pile become significantly larger. The plastic hinge of pile body appears when the maximum additional bending moment of pile reaches the ultimate bending moment, which is extremely dangerous to the existing bearing flexible pile that passes through thick layer of weak soils.