<sec>Bose-Einstein condensate (BEC) is essentially a macroscopic quantum effect with quantum volatility, macroscopic quantum coherence and artificial controllability. Owing to its unique controllability, it becomes a new ideal platform for quantum simulations and studies of interacting quantum systems.</sec><sec>In this paper, the generation of vortices and the formation of vortex chains, as well as characteristics of vortex chains in rotating two-dimensional BEC in a potential composed of harmonic potential and optical lattice are studied numerically. Firstly, the generation of vortices, the formation and distribution of vortex chains and the effects of different physical parameters on the vortex chains in two-dimensional BEC are investigated by using the multigrid preconditioned conjugate gradient method. Secondly, the evolution of the vortex chains with time is studied by using the time-splitting spectral method. The results show that the generation of vortices in BEC trapped in the compound potential corresponds to the minimum value of the potential. When the depth of the optical lattice increases to a certain value, vortex chains are formed in the BEC. With the further increase of the depth of the optical lattice, the vortex depth in the vortex chain in the BEC decreases continuously, and finally the vortex chain disappears completely. When the interaction strength between atoms increases, the distribution range of the condensate expands, and the number of vortices and the number of vortex chains in the condensate also increase. When the interaction strength between atoms increases to a certain value, the symmetry of the vortex chains is broken. As the rotation frequency of the condensate increases, the distribution range of the condensate expands, and the number of vortices and the number of vortex chains in the condensate also increase. When the rotation frequency is close to the external trapping potential frequency, the linear alignment of the vortex chains is disrupted. It is also found that there are three stages in the evolution of the vortex chains in the BEC: in the first stage, vortex chains rotate together with the condensate, and the original chain distribution keeps unchanged; in the second stage, the phenomenon of vortex space extrusion appears, and the vortex chain is destroyed; in the third stage, the phenomenon of vortex space expansion occurs, and finally the vortex chains disappear. The results above show that the depth of the optical lattice, the interaction strength between atoms, and the rotation frequency of the condensate have important effects on the vortices and vortex chains in the condensate. By adjusting these physical quantities, the number of vortices and the shape of vortex chains in the BEC can be effectively manipulated. This may provide some theoretical reference and guidance for future experiments and applications.</sec>