It is common in nature for birds or insects to fly in flocks. This study sought to understand the interaction mechanism between complex flows and the aerodynamic characteristics of flocks of flying organisms by employing the lattice-Boltzmann method to investigate tandem self-propelled flapping wings with an angle of attack of 10°. The effects of the initial heaving phase, the initial spacing between the fore and hind wings, and the phase difference between the heaving motions of the fore and hind wings were investigated. It was found that when the fore and hind wings flap in phase, the initial heaving phase and initial spacing can influence the final locomotive state of the tandem system, resulting in three modes: stable flight, collision, and separation. When the tandem system eventually achieves stable flight, only one equilibrium state is observed. In this equilibrium state, the trailing-edge vortex generated by the fore wing reattaches to the lower surface of the hind wing, resulting in 82.3% lower lift efficiency but 19.9% higher propulsive efficiency when compared to a single wing. When the fore and hind wings flap nearly out of phase, the tandem system has better lift characteristics while maintaining good propulsive performance. These findings improve the understanding of the principles of lift and thrust generation in flock flight and will help guide the design of bionic micro air vehicles.