With the development of railway transit networks, the number of twin shield tunnelling undercrossing intercity high-speed railway (HSR) is increasing. However, the understanding of the settlement mechanism of HSR subgrades induced by shield tunnelling undercrossing is still limited. Based on the case of twin tunnels passing through the Xulan HSR in Xi'an, China, a three-dimensional (3D) elaborate finite element model is established in this paper considering HSR subgrades, CFG pile reinforcement area (CFGPRA) and twin shield tunnels. The rationality and validity of the numerical results were verified by comparison with field measurements. The settlement and development process of HSR tracks caused by shield tunnelling were analysed. Additionally, some studies were performed on the internal force of CFG piles before and after tunnelling. The results show that the soil settlement near the tunnel crown in the CFGPRA model was approximately twice that in the greenfield stratum at the same depth. The settlement transfer in the CFGPRA appears in a “linear interval”. This suggests that the settlement near the top of the shield tunnel can be directly transferred to the surface in a linear manner. However, the transfer mode of deep strata subsidence to the surface is gradual line development. On this basis, two settlement rate indices (tangent slope and secant slope) were defined to obtain the specific range of the “linear interval”, which is 75% of the original pile length. Moreover, based on the mechanical analysis of the CFG piles, the relationship between the effective length of the piles and the linear interval was determined. The results obtained in this paper can provide an important reference for similar projects of shield tunnel undercrossing HSR.