Abstract Global climate change, species invasion, and human activities such as the construction of hydraulic facilities are contributing to the worldwide degradation of fish stocks. As a pivotal environmental factor that affects fish migration and population distribution, the low‐velocity flow has not drawn enough attention despite its extensive presence in various ecoregions. To understand the behavioural profiles of fish in low‐velocity flow, we examined the motility and swimming performance of two representative cyprinids, grass carp (GC, Ctenopharyngodon idella) and silver carp (SC, Hypophthalmichthys molitrix), under the combined effect of different flow velocities and illuminance ranges. The two species were exposed to two flow velocities (0.15 and 0.25 m/s) and three illuminance ranges (100.0–0.9 lx, 300.0–2.5 lx, and 700.0–4.9 lx). A novel behavioural metric, composed of light preference, swimming speed, rheotaxis index (RI), swimming stability (SS), and the probability of moving forwards/backwards over a certain distance (PMf‐0.1 and PMb‐0.1), was developed to fully characterise the motion strategy of fish. By analysing the individual distribution in light gradient, we confirmed the scototaxis of GC and found the oscillating light preference in SC that changed from 84.41–10.18 to 6.00–2.08 lx and disappeared with increasing illuminance. The RI and SS increased at the fast flow velocity (0.25 m/s) for both species, and SC was more forward‐prone and more stable than GC. Despite the fluctuating light preference, the higher illuminances heightened the RI and SS in SC, while in GC, higher illuminances inhibited the SS and had no impact on the RI. The results of PMf‐0.1 and PMb‐0.1 indicated that a higher flow velocity could facilitate the temporary upstream swimming in both species, while illuminance could only promote the same effect in SC. Finally, our study proposed possible manoeuvres in fine‐scale spatio‐temporal scenarios such as attraction flow and non‐traditional passages and provided valuable insights into fish community dynamics, laying the groundwork for alleviating the threat from invasive species and for future fish population recovery.