This manuscript proposes a method for studying resistance to the flow and thrombogenic properties of coatings based on collagen and carbon nanotubes formed by technology spray deposition. The development of a microfluidic chip that allows tight contact between the low-volume fluid and the coating in the microchannel facilitated in vitro testing of coatings under dynamic model fluid flow conditions. The type and structure of the flow inside the microfluidic chip channel were determined. Numerical modeling made it possible to determine the field of velocities in the section at the half-height of the microchannel and the shear stress on the lower wall of the microchannel at fluid pressure of 200 kPa. The constructed microfluidic system along with the connected microfluidic units allowed evaluating the properties of the coatings by simulating the closed blood flow for several hours. The dependence of resistance on the presence of the cross-linking agent, glutaric aldehyde, in the coating composition was demonstrated. Optical profilometry revealed that the coatings have sufficient resistance to high flow shear stress and are characterized by a roughness value of the same order as the titanium surface. Raman spectroscopy showed better anti-thrombogenic properties of the coatings relative to titanium.