The purpose of this study is to prevent the uplift of salt and sand in the areas exposed after the desiccation of the Aral Sea and to improve ecological conditions in the region. Research conducted in the Aral Sea zone has shown that, among desert plants, black saxaul (Haloxylon aphyllum) demonstrates superior effectiveness on saline soils due to its ability to strengthen the soil layer with its roots during survival and growth, as well as its capacity to block shifting sands. However, since the germination period of this plant species coincides with the sharp reduction of soil moisture in the newly exposed areas of the dried Aral Sea, the efficiency of germination under conventional sowing methods is decreased. Hence, experimental treatment aimed at accelerating germination during the period of normal soil moisture (February to March) was conducted using He–Ne (λ = 632.8 nm) and diode (λ = 532 nm) lasers. For laser-based ecological biotechnology treatment of black saxaul, exposure durations of 3 s, 6 s, 9 s, 15 s, 30 s, and 45 s were selected. According to the results of the experiment, the 3×30 algorithm produced the most effective outcomes compared to the other algorithms. Under the 3×30 algorithm using the He–Ne laser, germination compared to the control increased from 42.22% to 72.22%; the number of seedlings that emerged within the first 10 hours increased from 0 to 15; the total number of germinated seeds increased from 38 to 65; and the energy retention period increased from 7 to 17 days. Under the 3×30 algorithm using the diode laser, germination increased from 42.22% to 90%; the number of seedlings emerged within the first 10 hours increased from 0 to 31; the total number of germinated seeds increased from 38 to 81; and the energy retention period increased from 7 to 25 days. Two years of field trials confirmed enhanced establishment, with laser-treated seeds germinating within 10 days compared to no germination in controls.