To clarify the physiological mechanism of different groundwater depths affecting soybean evapotranspiration, photosynthetic characteristics and yield, a field experiment with four groundwater depth levels (1 m (D1), 2 m (D2), 3 m (D3) and 4 m (D4)) was conducted through the groundwater simulation system in 2021 and 2022. In this study, a quantitative analysis was conducted on the groundwater recharge and irrigation water demand and evapotranspiration (ET) of soybean fields with different treatments, and the effects of different treatments on soybean leaf area index (LAI), chlorophyll content index (SPAD), intercepted photosynthetic active radiation (IPAR), photosynthetic gas exchange parameters, dry matter accumulation (DMA) and yield were explored. The results showed the following: (1) Groundwater depth affected soybean ET and the source of ET. With the increase in groundwater depth, groundwater recharge and its contribution to ET gradually decreased, but the amount of irrigation required gradually increased, resulting in the ET as D1 > D4 > D2 > D3. (2) Soybean LAI, SPAD and IPAR were significantly affected by the different groundwater depths, of which the D1 treatment always maintained the maximum, followed by the D4 treatment, and the D3 treatment was the minimum. The photosynthetic gas exchange parameters under different treatments changed synergistically, showing significant differences in the flowering and podding stages, notably D1 > D4 > D2 > D3. Soybean DMA and yield first decreased and then increased with the increase in groundwater depth, and the average DMA and yield under the D1 treatment increased by 27.71%, 46.80% and 22.82% and 20.29%, 29.91% and 12.83% in the two years, respectively, compared to the D2, D3 and D4 treatments. (3) The structural equation model demonstrated that the groundwater depth indirectly affected the growth of soybean leaf area by affecting groundwater recharge, which in turn regulated soybean ET and photosynthetic capacity and ultimately affected DMA and yield. The above results showed that in the case of shallow groundwater depth (D1), the largest groundwater recharge promoted the growth of soybean leaf area and chlorophyll synthesis and increased the absorption and utilization of solar radiation. And it improved the leaf stomata conditions, accelerated the gas exchange between the plant and atmosphere, enhanced the photosynthetic production capacity and ET and achieved maximum DMA and yield. Soybean leaf growth and photosynthesis diminish with the increase in groundwater depth. In the case of deep groundwater depth (D4), the maximum irrigation improved the growth and photosynthetic performance of soybean leaves, which was favorable to ET, and ultimately led to increases in DMA and yield.