With the potential continuous application of mono- or few-layered black phosphorus (BP) in electronic, photonic, therapeutic, and environmental fields, the possible side effects of BP on aquatic organisms after release into natural water are of great concern. We investigated the potential toxicity of BP on the unicellular organism, Tetrahymena thermophila. After the exposure for 8 h at 10 μg/mL, the reproduction of T. thermophila significantly decreased by 46.3%. Severe cell membrane and cilium damage were observed by scanning electron microscopy (SEM) upon treatment with BP. Based on bright-field microscopy and three-dimensional Raman imaging, we investigated the cellular uptake and translocation of BP within T. thermophila. It was observed that the engulfment of BP by T. thermophila was oral apparatus dependent, through which intracellular BP was then transported to the posterior end of T. thermophila by food vacuole packaging. Our study also revealed that BP induced the increase of intracellular reactive oxidant species and formed oxidative stress-dependent toxicity to T. thermophila. Our findings paved a way for better understanding the BP toxicityon aquatic organisms and its potential ecological risks.