In this work, a semihydrodynamic (SHD) injection method was introduced and coupled with high salt stacking and electrokinetic chromatography for the analysis of estrogen and estrogen binding using a simple cross microchannel. The SHD method allows all samples to be hydrodynamically injected and focused into the separation channel at a relatively high flow rate and without splitting and diffusion, leading to reproducible bias-free injections of larger sample volumes (up to 50 nL) within 3 s. Moreover, the injection method is initiated without voltage switching, leading to a reduced mixing effect. Such advantages are well suited for performing stacking and sweeping on a microchip. We investigated the stacking effect under continuous and discontinuous co-ion conditions as well as under sweeping conditions. Micellar sweeping effect alone was relatively weak (7-8 times), partly due to a lower sodium cholate concentration (30 mM) used for the running buffer. By combining the sweeping effect with high salt stacking, however, up to a 200-300-fold enhancement factor could be achieved, and the high-salt and low-surfactant contents for the running buffer were favorable for binding study under nonequilibrium conditions. To the best of our knowledge, this is the first demonstration of the hydrodynamic injection used for high salt sample stacking on a microchip, also for further combining micellar electrochromatography and affinity separation for the analysis of hydrophobic ligand binding using microchip electrophoresis.