In this paper, the measurement performance of ions in electrophoresis microchips with different crosses was comparatively analyzed by simulation and experimental methods for the first time. Three types of microchips, including electrophoresis microchips with a traditional cross (EMTC), electrophoresis microchips with a double- I' cross (EMDC) and electrophoresis microchips with a cambered cross (EMCC), were fabricated. Several regulations of the cross-shape-effects on the measurement performance were obtained in the simulation and experimental results. The signal peak height and peak width of the measured ions grow with the increase of the radius for EMCC. And similar conclusions were gained for EMDC. However, the migration time of the separated ions was linearly proportional to the radius for EMCC while it showed slight fluctuation for EMDC. The proposed EMCC or EMDC showed much higher sensitivity and lower distinguishability compared to the EMTC. The results obtained in this paper gave us an in-depth and comprehensive understanding about the effects of the cross shape on the measurement performance in electrophoresis microchips. Meanwhile, the research results concerning the cross-shape-effects provided us a guidance to choose appropriate structures and fabrication processes for electrophoresis microchips.