The present invention discloses a gel electrophoresis chip, comprising a first substrate, a first plurality of parallel gel strips formed on the first substrate, respectively extending along a first direction and having a certain width; and a second plurality of isolation segments formed on the first substrate, respectively located between adjacent gel strips and extending along a second direction different from the first direction, the isolation segments being arranged to form a microwell array together with the gel strips. After the gel electrophoresis chip achieves conventional protein two-dimensional gel electrophoretic separation, protein samples suitable for mass spectrometry analysis are prepared in high throughput, thus greatly reducing the pretreatment time of mass spectrometry analysis, thereby being suitable for proteomic analysis of biological samples.