Wildlife crossing structures (WCSs) are widely adopted for alleviating the negative impacts caused by anthropogenic linear infrastructures (ALIs). However, research on canal WCSs in desert environments remains scarce, particularly regarding how anthropogenic disturbance influences their utilization by desert mammals. Using long-term camera trap monitoring data from northern Xinjiang, China, we examined the dynamics of desert mammals in utilizing canal WCSs. Leveraging the quasi-experimental conditions created by COVID-19, we investigated the changes in encounter rates, activity patterns and potential predator-prey interactions before, during and after the lockdown. Focusing on four focal species (Red fox Vulpes vulpes, Goitered gazelle Gazella subgutturosa, Gray wolf Canis lupus and Tolai hare Lepus tolai), we observed annual activity periodicity and increased encounter rates during lockdown. Activity patterns shifted in species-specific ways, influenced by diel phenotypes. Predator-prey interactions were further complicated by changes in anthropogenic disturbance. Our findings highlight how local environments and species traits jointly shape wildlife responses to anthropogenic disturbance. Species-specific reactions during the pandemic were influenced by tolerance to anthropogenic disturbance, reflected in functional traits and population statuses. Changes in predator-prey interactions, such as more distinct avoidance behaviours, can exacerbate the system instability, which further underscores the importance of minimizing human impact. Practical implication. Our research represents a pioneering effort in understanding the impacts of COVID-19 lockdown on wildlife utilization of canal WCSs. The findings may guide ecological conservation efforts and inform effective WCSs construction in arid regions. We recommend implementing vehicle management measures and enhancing structural complexity to alleviate the negative impacts of anthropogenic disturbance and improve WCSs performance.