| Obstacles create a complex flow environment in fishway. Understanding swimming behavior in complex flow environment is critical to improving the effectiveness of fishways. In this study, the swimming kinematics of juvenile silver carp holding station and moving forward under obstacle conditions were analyzed in different flow velocities (1 BL/s，3 BL/s and 5 BL/s) (body length per second). Metrics used to quantify kinematics were tail-beat frequency, tail-beat amplitude, ground swimming speed, swim acceleration, and ground stride., Compared to free stream swimming at flow velocity of 3 BL/s, silver carp holding station behind the obstacle showed a significant decrease in tail-beat frequency and significant increase in tail-beat amplitude; silver carp moving forward behind the obstacle showed a significant decrease in tail-beat frequency, ground swimming speed, swim acceleration and ground stride, and significant increase in tail-beat amplitude. This result showed that the obstacle help fish to save energy at 3 BL/s. In the obstacle-placed currents, tail-beat frequency of the holding station behavior increased with flow velocity. Tail-beat frequency, tail-beat amplitude and swim acceleration of moving forward behavior increased with flow velocity, while ground stride decreased with flow velocity. At flow velocity of 3 BL/s, we found that silver carp positioned a preferential position from 5-30 cm downstream of an obstacle where fish might adopt Karmen gait, and residence time accounted for 92.5%. At flow velocity of 1 BL/s and 5 BL/s, silver carp did not have an evident preferential position in the flume. Silver carp often closed to the wall to swim, and there was no obvious position preference. Our results indicate that a certain combination of obstacles and flow velocity will create flow refuge for fish to exploit. The results provide important reference for fishway design.