The invention discloses a method for preparing mercapto-functionalized polyester using a micro-reaction device, which uses δ-valerolactone (VL) or ε-caprolactone (CL) as a reaction monomer, tin trifluoromethanesulfonate ( Sn(OTf) 2 ) is a metal complex catalyst, and the aliphatic alcohol with a mercapto group as a terminal group is a functional initiator, which is prepared in a microreactor. Compared with the prior art, the metal complex catalyst adopted in the present invention is simple and easy to obtain, has high catalytic activity, and the process of the present invention has strong operability and low cost. At the same time, the present invention has short polymerization process time, high reaction conversion rate, high polymer mercapto group introduction rate and high-precision control of polymerization reaction.