In this study, the blood cell clogging phenomenon occurring in blood separators based on capillary action is carefully investigated and how to minimize the reduction in plasma separation speed caused by clogging is discussed. Four different blood separators are fabricated on optically transparent glass substrates to clearly observe the blood plasma separation and the blood cell clogging in the microfluidic devices. Each separation experiment is captured by a high-speed video camera. The captured images are analyzed using a theoretical model proposed in this study to quantify the effect of the microstructure on the degree of blood cell clogging. Finally, design guidelines for the microstructure of the micro blood separator are discussed based on the analysis.