The invention provides an operation method of a rail on-site flash welding and post-welding heat treatment integrated machine. The operation method includes the steps of: 1, a control device controlsa steel rail clamping part assembly to clamp and align two steel rails to be welded; 2, flash welding, upsetting and weld seam shearing are carried out; 3, the control device controls a heating coil of a heat treatment machine head assembly to align with a welding joint for heat treatment; and 4, the integrated machine resets. According to the operation method of the rail on-site flash welding andpost-welding heat treatment integrated machine, integrated operation of welding and heat treatment procedures is achieved; operation machinery, procedures, scheduling, personnel and time are reduced;joint welding quality is guaranteed; and overall operation efficiency is improved.