In this paper, we propose a novel idea of controlling microstructure and mechanical properties based on the non-equilibrium microstructure of nickel-based superalloy fabricated by laser powder bed fusion (LPBF). The network microstructures were firstly built in LPBF nickel-based superalloys by direct aging (DA) heat treatment. Thermodynamic calculations were conducted to design the DA and homogenizing + DA (HDA) heat treatments for elucidating the control mechanism. The results showed that the non-equilibrium microstructures in as-built nickel-based superalloy contributed to the network microstructure formation and recrystallization during DA heat treatment. The grains were refined and the <001> texture was eliminated after DA heat treatment. The non-equilibrium microstructures were removed and the recrystallized grains tended to coarsen after HDA heat treatment due to high temperature homogenizing treatment. The in-situ nano γ′ phase uniformly distributed in the grains of HAD-treated microstructures, which was also found inside network microstructures of DA-treated microstructures. Due to the additional strengthening effect of refined grains and network microstructures, the strength of DA-treated sample was higher than those of as-built and HAD-treated samples, while the ductility was lower than that of as-built sample, and but was close to that of HAD-treated sample. This study will provide guidance for developing a suitable heat treatment process of LPBF nickel-based superalloys.