The invention discloses a method for manufacturing a three-dimensional ceramic micro device. The method includes manufacturing a polydimethylsiloxane (PDMS) elastic mould to replace a conventional hard mould; preparing ceramic slurry high in solid phase content and low viscosity; adding the ceramic slurry into the PDMS elastic mould, and adopting a centrifugal assisted micro moulding method for injection moulding; adopting a plastic thin film as a substrate to replace a conventional ceramic substrate for drying; completing the process through demoulding and sintering. Advantages of soft etching technology and powder metallurgy technology are combined, the plastic thin film is adopted as the substrate for the first time to replace the conventional ceramic substrate for drying, and the centrifugal assisted injection moulding method is provided, so that the method has the advantages of low production cost, simplicity and quickness in experimental operation and high reliability and can be used for manufacturing the three-dimensional ceramic micro device.