The invention relates to the technical field of fuel cell vehicles, in particular to a fuel cell vehicle tail gas and water vapor separation and emission system and a control method thereof. The tailgas and water vapor separation and emission system comprises a fuel cell stack, a tail gas conveying pipe, a water tank, a fuel cell control unit, a first control switch, an exhaust pipe and a drain pipe, one end of the tail gas conveying pipe is communicated with the tail gas output end of the fuel cell stack, and the other end of the tail gas conveying pipe is communicated with a gas inlet of the water tank; the exhaust pipe is communicated with a gas outlet of the water tank, a filter unit is arranged at one end, far away from the water tank, of the exhaust pipe, the filter unit is used forfiltering gas, the drain pipe is communicated with a water outlet of the water tank, and the first control switch is arranged on the drain pipe and used for connecting or disconnecting the drain pipe. Liquid separated by the system is collected in a centralized mode, regular and fixed-point drainage is conducted, and the problem that in the prior art, tail gas is discharged at will, and consequently the road surface environment is affected is solved.