The invention discloses a high molecular weight aliphatic polycarbonate copolyester and a preparation method thereof, and relates to a multi-step ester exchange reaction and a high-temperature high-vacuum polycondensation reaction of aliphatic polyhydric alcohols, 2,5-furandicarboxylic acid and carbonic acid aryl esters. The ester exchange reaction and the polycondensation reaction are implemented continuously, so that the ester exchange reaction time is shortened, the equipment utilization rate is improved, no extra catalyst is needed before polycondensation, and thus the experiment steps are simplified. According to the copolyester disclosed by the invention, furandicarboxylic acid polyester structure units or chain segments are introduced into aliphatic polycarbonate main chains, so that the copolyester has the biodegradation of the aliphatic polycarbonate and excellent thermodynamic and processing proprieties of the furandicarboxylic acid polyester simultaneously, defects that the aliphatic polycarbonate is low in glass-transition temperature, low in melting temperature, low in crystallization temperature and the like are overcome, and requirements of different industries are met.