The invention relates to a color polyester cotton compound superfine fiber manufacturing process. The color polyester cotton compound superfine fiber manufacturing process is characterized in that the manufacturing process comprises the following steps: firstly, the raw material polyester fiber and the nylon are sliced; secondly, the sliced polyester fiber and the nylon are dried with a crystallization dryer; thirdly, coloring material particles are added to the crystallization dryer through a color printing machine to perform drying; fourthly, the dried polyester fiber slices, the nylon slices and the coloring material particles are melted with a screw rod extruding machine; fifthly, the melted body volume is controlled through a spinning finish measuring pump and a spinning measuring pump; sixthly, compound spinning is performed on a conjugated spinning machine; seventhly, after spinning, the fiber is rolled into a spinning cake through an automatic high speed winding machine; eighthly, the winded spinning cake is placed in a balancing chamber to be balanced; and ninthly, texturing is performed to the balanced spinning cake on a common texturing machine. Compared with the prior art, the process has the advantages that the coloring can be directly realized during the spinning process, the color fastness, the sunlight fastness and the thermal fastness are good, the gloss is even, and the color rendering property is good.