The sand intrusion in railway tracks in sandy regions can significantly change the mechanical behaviour of tracks and thus threaten the safety of train operation. This paper presents substantial field tests on both sandy and clean railway tracks to study the effect of sand intrusion on the longitudinal resistance of ballast bed and the vibration behaviour of track structures. After that, a 3D multi-scale the discrete element model is developed to study the micro-contact between ballast particles and the vibration behaviour of sandy tracks during train passing in detail. Also, the effect of train speeds and axle loads on the mechanical behaviour of sandy tracks is discussed. The results show that the sand intrusion increases the vibration acceleration amplitude of rail and sleeper by 11.3% and 50.3%, while ballast bed decreases by 44.9%. Besides, the sand intrusion significantly changes the energy distribution in the track, wherein the frequencies of the highest energy of rail and sleeper are increased while that of the ballast bed is decreased. The parametric study shows the high train speed can cause the increase in overall acceleration of the ballast bed and high axle load can cause an increase in the micro-contact forces between ballast particles, diffusion angle of the contact force chain, displacements of ballast particles, acceleration of ballast particles, and sleeper displacements.