As traditional slab gel electrophoresis has some disadvantages such as tedious operation steps，long experimental time and possible damage to human health from ultraviolet light，a rapid gel electrophoresis system was developed based on electrophoresis biochip，which could realize the separation and imaging of DNA by adding the DNA sample into the biochip.Taking the 20，50 and 100 bp DNA ladder as target compounds，the DNA fragments were separated in the gel electrophoresis system，and the optimal electrophoretic parameters were as follows:the electric field strength:100 V/cm，the agarose mass concentration:1%.Results showed that all the DNA samples could be efficiently resolved in 14 min with the correlation coefficient between migration distance and the DNA size higher than 0.91.Besides，the instrument could run with a good stability.