Non-Newtonian fluids are widely used in microfluidic systems and biomedical fields. In this paper, based on molecular dynamics simulation, taking the system composed of sodium carboxymethyl cellulose molecules and water molecules as the research object, the configuration evolutions of sodium carboxymethyl cellulose solution are simulated under different shear rates. Change of the solution viscosity is characterized by mean square displacement of sodium carboxymethyl cellulose molecules and the relative velocity between water layer and shear boundary. The effect of hydrogen bonding on the viscosity of the solution is analyzed emphatically. The results show that water molecules and solute molecules attract each other to form a more compact hydrogen bond network, which increases the viscosity of the solution; the peak value of the radial distribution function between the hydrogen atoms attached to carbon and the water oxygen atoms decreases when shear action is applied to the solution, and the hydrogen bond between the two atoms is weakened; the mobility of solute molecules increases and the blocking effect of water molecules on the movement of solute molecules weakens under the shear action; at the same time, the shorter the distance to the shear boundary, the closer to the shear velocity the velocity of water molecules is, and with the increase of distance, the velocity of water molecular layer decreases greatly. These results are macroscopically understood as the viscosity of the system decreasing. As the shear rate increases, the shear thinning of the sodium carboxymethyl cellulose solution becomes more significant.