Polycyclic aromatic hydrocarbons (PAHs) are a class of organic pollutants widely present in aquatic environments. Phenanthrene (Phe), a notable PAH, has attracted significant attention due to its environmental toxicity and bioaccumulation potential. Misgurnus anguillicaudatus, an important freshwater aquaculture species in China, was used as the model organism to study the effects of Phe stress on locomotor activity, anxiety-like behavior, and social behavior. The experiment established four Phe concentration treatment groups (0.2, 1.0, 5.0, and 25.0 μg/L) for toxicity exposure. Behavioral changes were assessed at 15, 30, and 45 days of exposure, as well as after a 30-day recovery period. An animal behavior tracking system recorded velocity, turn angle, angular velocity, cumulative duration time ratio in black and white areas, and cumulative duration time ratio in social and non-social areas. A generalized linear mixed model (GLMM) analyzed the effects of Phe stress duration and concentration on behavioral indicators. Phe stress significantly affected the locomotor activity, anxiety-like behavior, and social behavior of M. anguillicaudatus: Locomotor behavior. At 15 days of exposure, the velocity of M. anguillicaudatus significantly increased in the 0.2, 1.0, and 5.0 μg/L Phe groups. By 45 days, velocity significantly decreased in the 1.0 μg/L group but increased in the 25.0 μg/L group. The turn angle significantly decreased in the 0.2 μg/L group at 15 days, while angular velocity significantly increased in the 1.0 μg/L group. In the 5.0 and 25.0 μg/L groups at 30 days, both turn angle and angular velocity significantly increased. GLMM analysis revealed that exposure time had a highly significant effect on velocity, while concentration significantly influenced turn angle and angular velocity. After 30 days of recovery, velocity in the 1.0, 5.0, and 25.0 μg/L groups remained significantly higher than in controls, and turn angle and angular velocity in the 5.0 μg/L group stayed elevated, indicating lasting impacts on directional changes. Anxiety-like behavior. At 15 days, the cumulative duration time ratio in the black area significantly decreased in the 0.2 μg/L group but increased in the 1.0 μg/L group. By 30 days, the ratio significantly increased in the 25.0 μg/L group, and at 45 days, it increased in the 1.0 and 5.0 μg/L groups. GLMM confirmed that exposure time had a highly significant impact on anxiety-like behavior. After recovery, all treatment groups showed a significantly higher cumulative duration time ratio in the black area compared to controls, suggesting persistent anxiety-like effects. Social behavior. At 15 days, the cumulative duration time ratio in the social area significantly decreased in the 0.2 and 25.0 μg/L groups. By 30 days, the ratio in the non-social area significantly increased in the 1.0 μg/L group, and at 45 days, it decreased in the 5.0 μg/L group. GLMM indicated that Phe concentration had a highly significant effect on social behavior. After recovery, the 5.0 and 25.0 μg/L groups still exhibited a significantly higher ratio in the non-social area, demonstrating persistent and irreversible social inhibition. Phe stress exhibited time- and concentration-dependent effects on M. anguillicaudatus. Short-term exposure to low-concentration Phe inhibited turning ability, while long-term exposure to higher concentrations increased turning ability and velocity. Phe stress significantly induced anxiety-like behavior and suppressed social behavior, with these changes showing persistence and irreversibility. This study provides insights for assessing the ecological risks of Phe, establishing water quality standards based on fish behavior, and improving monitoring techniques for PAHs in aquaculture environments.