The refractive index structure constant, as one of the key indicators characterizing atmospheric turbulence intensity, is measured by the temperature pulsation meter. Research on its measurement uncertainty is of significant importance. Based on the principle of the temperature pulsation meter, a tungsten filament with a diameter of 10 μm, a resistance value of 90 Ω and a temperature coefficient of variation of 4.5×10^-3/K were used as the measuring sensor to obtain the average temperature different coefficient. The measurement uncertainty of refractive index structure constant was derived from an integrated analysis of parameters including pressure, temperature and distance. Experimental data indicates that within the true value range of 10^-13 to 10^-16 near the ground, the calculated measurement uncertainty remains within 1%, demonstrating its reliability. The result is very effective for improving the measurement resolution of temperature pulsation meter, and it is also a new idea for controlling the measurement uncertainty of temperature pulsation meter.