This study was conducted to evaluate the Al3+ tolerance of sixteen camelina genotypes and to use melatonin or nano-selenium to alleviate Al3+-induced stress. A Petri dish study indicated seedling root length was suitable for describing the dose–response of seedling growth with increased Al3+ concentrations. Based on GR50 (Al3+ concentration causing a 50% reduction in the seedling root length), CamK6 (232.0 mg L−1) and CamK2 (97.0 mg L−1) were the most Al3+-tolerant and -sensitive genotypes, respectively. Under Al3+ stress, CamK6 and CamK2 treated by melatonin (50 μM) or nano-Se (0.4 mg L−1) showed a similar plant height and seed yield plant−1 (CamK6: 123.6 ± 9.8 cm and 0.562 ± 0.62 g; CamK2: 109.2 ± 8.7 cm and 0.49 ± 0.5 g) as the controls (CamK6: 121.1 ± 10.2 cm and 0.554 ± 0.4 g; CamK2: 110.0 ± 9.8 cm and 0.5 ± 0.4 g), and the values were greater than for the Al3+-treated plants (CamK6: 96.4 ± 9.2 cm and 0.48 ± 0.34 g; CamK2: 97.3 ± 8.1 cm and 0.42 ± 0.31 g). The results showed that melatonin or nano-Se through modulating biochemical reactions (e.g., antioxidant enzyme) can alleviate Al3+-induced growth inhibition in camelina. This study suggested melatonin or nano-Se can alleviate Al3+-induced growth inhibition by maintaining seed yield and improving oil quality in camelina.