The invention provides a micro-droplet type PCR (polymerase chain reaction) chip and a manufacture method thereof. The upper layer of the chip is a PDMS (polydimethylsiloxane) imaging cover plate formed by connecting a DNA (deoxyribonucleic acid) target fragment with a primer injection port, a single phase drop forming microstructure, a PCR reaction enzyme and an mRNA (messenger ribonucleic acid) substrate injection port, an oil phase reagent injection port, a drop straight line channel, a cross hybrid channel, a micro drop buffer channel, a micro drop PCR reaction chamber and a micro drop PCR waste liquid chamber, the lower layer of the chip is a glass substrate, and the upper layer and the lower layer are bonded and packaged to form a complete micro drop PCR chip. The manufacture method of the chip comprises the steps of firstly, manufacturing a mask plate; secondly, molding; thirdly, pouring a die; and fourthly, taking a figure. The PDMS figure at the upper layer of the chip adopts a multilayer filter structure, and the formed micro drop has a uniform size, stable grain diameter and strong controllability. Compared with traditional PCR chips, the micro drop PCR chip manufactured by the method has great advantages in hybrid effect, reaction efficiency, and high throughput.