In the process of high-concentration photovoltaic (HCPV) power generation, multijunction cells work in the conditions of high radiation and high current. Non-uniformity of focusing, the mismatch between the focusing spectrum caused by the dispersion effect and the spectrum of multijunction solar cell design and the increase in cell temperature are the key factors affecting the photoelectric performance of the multijunction solar cell. The coupling effect of three factors on the performance of multijunction solar cell intensifies its negative impact. Based on the previous research, the light intensity and spectral characteristics under Fresnel lens focusing are calculated through the optical model, and the optical–electrical–thermal coupling model under non-uniform illumination is established. The results show that obvious changes exist in the concentration spectrum distribution, energy and non-uniformity along different optical axis positions. These changes lead to serious current mismatch and transverse current in the multijunction solar cell placed near the focal plane which decreases the output power. The lost energy makes the cell temperature highest near the focal plane. In the condition of passive heat dissipation with 500 times geometric concentration ratio, the output power of the solar cell near the focal plane decreases by 35% and the temperature increases by 15%. Therefore, optimizing the placement position of the multijunction cell in the optical axis direction can alleviate the negative effects of optical–electrical–thermal coupling caused by focusing non-uniformity, spectral mismatch and rising cell temperature, and improve the output performance of the cell. This conclusion is verified by the experimental result.