Complex plasmas are composed of ionized gas and mesoscopic particles, representing a typical non-equilibrium complex system. The particles are negatively charged due to the higher thermal velocity of the electrons and interact with each other via Yukawa interactions. As the motions of individual particles can be easily recorded by video microscopy, generic processes in liquids and solids can be studied in complex plasmas at kinetic level. Under microgravity conditions, the particles are confined in the bulk plasma and form a three-dimensional cloud. In the PK-4 Laboratory on board the International Space Station, melamine formaldehyde particles of diameter 6.8 μm and 3.4 μm are injected consecutively in the plasma discharge. Due to the electrostatic force and ion drag force, usually, the particles cannot be mixed in the same region, leading to a phase separation. During the particle injections, small particles penetrate into the cloud of big particles, self-organizing differently under various conditions. When the number density of the big particles is low, small particles form a channel in the center of the discharge tube due to the Yukawa repulsion, where the cloud of the big particles is weakly confined. When the number density of the big particles is mediate, lanes are formed during the penetration of the small particles, representing a typical nonequilibrium self-organization. When the number density of the big particles is high, dust acoustic waves are self-excited due to the two-stream instability. As the small and big particles interact with each other, the particle number density in the wave crests rises drastically. However, the wave numbers and frequencies remain unaltered. This investigation provides insights to the different self-organizations during the particle injections in three-dimensional binary complex plasmas under microgravity conditions.