The invention discloses a safety linkage control method of a tunnel under-passing railway. The method includes: monitoring deformation condition of an existing railway in real time, dividing a whole construction process into a normal state, a forewarning state and a warning state according to the deformation condition of the railway, and continuing construction if the construction is in the normal state; if the construction is in the forewarning state, sending out a warning, and continuing construction after adjusting constructional parameters; if the construction is in the warning state, performing stopping, carrying out feasible suggestions proposed by experts, canceling the warning, and resuming work to control safety implementation of the tunnel under-passing railway. The invention further discloses a system implementing the method, which system comprises a full-automatic monitor module, a construction parameter acquisition module, a data sharing platform and a forewarning platform. Safety hazards occurring in the construction process are solved quickly and efficiently; by using the system, the defect that traditionally a single department independently solves problems is overcome, and inter-department safety awareness is enhanced; tunneling safety and efficiency is improved.