Due to the effect of atmospheric refraction, the space objects (e.g. stars, aircraft, and so on) observed from ground-based optoelectronic telescopes always have positions that different from their actual ones. The lower the elevation of the space objects, the more obvious the effect of atmospheric refraction becomes, and hence the larger position difference will be deduced. To position the space objects with high accuracy, it is necessary to correct the effect of atmospheric refraction. In order to improve the correction accuracy of atmospheric refraction effect during the observation of space objects with low elevations, the correction curves of atmospheric refraction effect were obtained by retrace-scanning fixed stars in the neighborhood of the orbit of space objects, based on the original model for correcting and computing the effect of atmospheric refraction. At last, through large amount of experimental demonstration and polynomial curve fitting, a new expression was proposed for the correction of atmospheric refraction effect with low elevation observation. The computation results from several experiments show that, during the observation of mission space objects with infrared long-wavelength system, the initial elevation reduced to 2° from 10°, the capture time for the mission space objects with infrared long-wavelength brought forward more than 50 s, and the critical characteristic points(e. g. assembly separation) of the mission space objects could be observed. The experimental results indicates that, our proposed method can be used to reduce effectively correction error of atmospheric refraction effect with low elevation observation, to improve the capability and accuracy in the process of capturing and tracking the mission space objects with infrared long-wavelength systems, and has great worth in actual engineering and practical application area.