Alternatively permutated conic baffles (APCB) were proposed to generate vertical and horizontal vortex flow to intensify mixing and mass transfer in a raceway pond. Both clockwise vortexes were generated before and after conic baffles in the main stream to increase perpendicular velocity by 40.3% and vorticity magnitude by 1.7 times on vertical cross section. Self-rotary flow around conic baffles and vortex flow among conic baffles were generated to increase perpendicular velocity by 80.4% and vorticity magnitude by 4.2 times on horizontal cross section. The bubble generation time and diameter decreased by 25.5% and 38.7%, respectively, while bubble residence time increased by 84.3%. The solution mixing time decreased by 48.1% and mass transfer coefficient increased by 34.0%. Vorticity magnitude and turbulent kinetic energy increased by 5.9 and 13.9 times, respectively. Besides, the detailed vortex structures of algal cells movement was clarified and optimized to improve the flashing light frequency. Numerical simulation showed that the peak vortex intensity appeared in the centre of APCB, while the peak solution velocity appeared in the middle of baffles spacing. The vortex diameter was mainly affected by relative spacing of conic baffles, while vortex centre was mainly affected by relative height of conic baffles. Particle image velocimetry (PIV) was used for the validation of vortex flow. Through optimizing the relative height and spacing of RWP-APCB, the flashing light frequency of algal cells and light fraction in light/dark cycle period increased by 1.0 and 3.1 times, respectively. The average light energy utilization efficiency and productivity per energy input increased by 24.7% and reached to 24% and 1.0 g/W/d, respectively. The CO2 fixation rate of algal biomass during harvesting in RWP-APCB promoted by 47.2% and reached to 3.5 g/L/d.