When measuring atmospheric optical turbulence with a balloon-borne micro-thermometer, the wake caued by the rising balloon will affect the measurement of the thermometer below it. In order to analyze this effect, experimental measurements were carried out in Huaihua, Hunan Province, China, in November 2021 using the method of hanging two radiosondes under a balloon. Fistly, the wake evaluation standard proposed by Barat was used to evaluate the effects of the wake at different positions under the balloon, and the turbulence intensity measured at different positions under the balloon was compared. Then, according to the measured refractive index structure constant, the coherence length and atmospheric seeing of different height were compared, and the measurement deviation comparison of different positions under the balloon was obtained. The results show that at altitudes of 0–6 km, the measurement result with a 30 m rope is significantly affected by the wake, at altitudes of 6–15 km, the balloon wake has little influence on the measurement due to larger wind shear, and at altitudes of 15–30 km, despite the existence of wake effects, they have little contribution to the optical parameters of the entire atmosphere due to the weak optical turbulence intensity in this altitude layer. This study has great reference significance for future sounding measurements of optical turbulence.