In this paper, a novel approach was introduced for cross flow fan design by incorporating bionic microstructures on the blade surface. Two types of bionic microstructures, riblet and convex hull, were constructed and studied to achieve high aerodynamic efficiency and low noise design. Numerical simulations were conducted to understand the influence of bionic microstructures on the fan’s aerodynamic and acoustic performance, and the impact of design parameters on these performances was investigated. After printing the bionic microstructure fan samples, the experimental tests were carried out. The flow field and sound field data of the fans with bionic microstructures and the original fan were compared. The results demonstrated that both riblet and convex hull microstructures effectively improved the fan’s aerodynamic performance by reducing turbulent kinetic energy on the blade surface. Additionally, the microstructures inhibited boundary layer separation on the suction surface of adjacent blades, which contributed to reducing vortex noise. However, the pressure gradient formed near the convex hull and the edge of the small-diameter riblet resulted in deterioration in the noise of the corresponding fan. By optimizing the diameter and spacing of the riblet microstructure, the best noise reduction performance was achieved for the riblet fan. The optimized fan showed a 5.3% increase in maximum air volume flow rate and a 2.4 dB(A) reduction in noise. Overall, the cross flow fan design method based on bionic microstructures has valuable application potential in improving the aerodynamic and acoustic performance of various rotating machinery.