This study investigated the effect of the Discovery Learning model integrated with a Deep Learning approach on students’ learning outcomes in the topic of Environmental Change and Conservation. A quasi-experimental design with a Non-equivalent Control Group was employed, involving 70 Grade X students at High School 1 Batang Kuis, Indonesia, divided equally into experimental (n = 35) and control (n = 35) groups. Instruments included 20 higher-order thinking (C4–C6) multiple-choice items administered as pretest and posttest. Data were analysed using the Mann–Whitney U test and Normalised Gain (N-Gain) through IBM SPSS Statistics. Results showed that posttest mean scores were significantly higher in the experimental class (M = 89.57, SD = 7.51) than in the control class (M = 82.14, SD = 10.79). The Mann–Whitney test yielded a significant difference (U = 280.5, p = 0.03), with the experimental group’s mean rank (42.67) exceeding that of the control group (28.33). Furthermore, the experimental class achieved a high N-Gain category (0.78) compared to the moderate category of the control class (0.66). These findings demonstrate that the Discovery Learning–Deep Learning integration effectively promotes conceptual understanding and higher-order cognitive skills in biology education.
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