The invention discloses a method for high-throughput detection of transgenic corn by virtue of a micro-fluidic chip. The micro-fluidic chip which contains not less than 20 reaction pores in each column of fluid channels and has not less than 3 columns of the channels, wherein the reaction pores of each column of the fluid channels are respectively embedded with 20 groups of specific primer probe compositions as shown in SEQ ID NO.1-60 in advance. According to the method disclosed by the invention, a TaqMan Array Card micro-fluidic chip detection technology is applied to the high-throughput screening detection of a transgenic corn line; in a polymerase chain reaction (PCR) amplification process, the screening detection of 2 corn endogenous genes and the screening detection of 18 exogenous recombinant lines are simultaneously completed, and the detection sensitivity can reach up to 1%. Compared with a single detection, the method can be used for detecting the endogenous genes and the exogenous genes in one PCR amplification reaction, thereby effectively avoiding possible errors caused by misoperation in experiments; and therefore the high-throughput screening detection of multiple samples and multiple gene targets can be achieved.