Thrombus formation on biomaterial surfaces with microstructures is complex and not fully understood. We have studied the micro-secondary flow around microstructures that causes components of blood to adhere physically in a low Reynolds number region. The purpose of this study was to investigate the effect of micro-column size on the adhesion phenomena and show a quantitative relationship between the micro-secondary flow and physical adhesion phenomena, considering microstructures of various sizes. The flow simulation and quantitative assessment of adhesion rates around micro-columns was conducted using four sizes of micro-columns. This study also calculated the vectors of micro-secondary flow and average shear rate around a micro-column using a computational fluid dynamics analysis. The simulation showed the micro-secondary flow toward the bottom surface at upstream side and low shear rate distribution generated around a micro-column. Furthermore, physical adhesion tests were conducted using microbeads and a perfusion circuit to examine the size effect of the micro-columns on the physical adhesion. The results showed that the average adhesion rate around the micro-column increases with the associated size increase of the micro-column. Our results indicate that quantification of micro-secondary flow on a material surface with microstructures of several sizes and shapes (such as in a rough surface) is important for the evaluation of the adhesion phenomenon even though the surface roughness value on the material surface is small.