The invention discloses a FACTS and OLTC online voltage coordination control method coping with wind power fluctuations and a system thereof and belongs to the electric power system safety stabilization technology field. The method is characterized by through coordinating and controlling a main station in an on-line mode, after a wind speed prediction curve in a future period is acquired, calculating a total voltage deviation of a system; and through carrying out perturbation on OLTC motion and voltage changes, according to a perturbation result, determining an OLTC motion strategy so that the total voltage deviation of the system is continuously decreased; based on the above condition, calculating a sensitivity matrix of reactive compensation changes of each FACTS equipment to a bus voltage of each voltage check point; taking a minimum FACTS equipment reactive compensation variation quantity and a minimum voltage deviation as optimization targets and calculating a FACTS motion strategy. In the invention, OLTC and FACTS voltage regulation means can be combined to realize stable control of the voltage.