The invention provides an integrated temperature controlled PCR-CE (polymerase chain reaction-capillary electrophoresis) micro-fluidic chip and a preparation method thereof. The chip adopts a double-deck design, an upper layer is a PCR and CE reaction channel made of PDMS (polydimethylsiloxane) material, a lower layer is a platinum electrode substrate obtained through a micromachining technology, so that the temperature for PCR is detected and controlled circularly, the upper layer and the lower layer are formed by degumming and packaging through PDMS semi-solidification and plasma, and the whole chip integrates three processes of temperature control, PCR amplified reaction and CE separation. According to the method, portable chips integrating PCR and CE can be prepared, so that DNA segments and target genes are convenient to amplify, the chip has the characteristics of accurate temperature control, fast reaction speed, small use level and high integration, has relatively low preparation cost, and can obtain rapid and reliable PCR reaction data.