The invention discloses a working medium filling system for an independent parallel multichannel flat heat pipe, and a filling method thereof. The filling system comprises a working medium tank, a quantitative system, a constant temperature common chamber, a flat heat pipe, a variable temperature system, a vacuum system and a sealing system; and control valves are arranged between the quantitativesystem and the constant temperature common chamber as well as between the constant temperature common chamber and the vacuum system. During filling, non-condensable gas in a pipeline system and the flat heat pipe is pumped out firstly, and then high temperature and high pressure working medium vapor is filled into the flat heat pipe through the quantitative system; when temperature and pressure vapor-liquid equilibrium is achieved, working media in the parallel multichannel flat heat pipe are in the vapor-liquid phase coexisting state; at the moment, one end of the parallel multichannel flatheat pipe is sealed through the sealing system, so that the independent parallel multichannel flat heat pipe is made. The working medium filling system has the advantages of stable overall performance, the high filling quality and automation degree, and the simple technology, and is suitable for mass production, and the mass consistency of the working media in each flat heat pipe channel can be controlled accurately.