Adding baffles inside raceway photobioreactors is a method to strengthen mixing. In this paper, a new type of staggered baffles are designed and compared with other structural baffles. Computational fluid dynamics was used to analyze the mixing effect of baffles with different structures in the raceway photobioreactors. The light–dark cycle of the staggered baffles was analyzed by coupling the motion trajectories of dynamical proton model particles through the change of outdoor light intensity during the day. The light–dark cycle of the cross baffle was analyzed according to the change of outdoor light intensity during the daytime coupled with the motion curve of dynamical proton model particles. The mixing ability of the staggered baffles was verified by mixing time, mass transfer coefficient, and outdoor cultivation. The results show that when the speed of the paddlewheel reached 20 rpm, compared with the raceway photobioreactors without baffles, vorticity increased by 23.3% respectively; the light–dark cycle period reduced by 18%; the mixing time reduced by 40%, and the mass transfer coefficient increased by 9.67%, the biomass of Chlorella increased by 25.3%. Compared with the other two baffle structures, the light–dark cycle period was reduced by 7.3% and 5.9%, the mixing time was reduced by 15% and 8%, and the mass transfer coefficient was increased by 1.17% and 3.59%. The biomass increased by 8.3% and 4.8%. The staggered baffles have better mass transfer performance, which can provide a reference for the optimal design of raceway photobioreactors.