Magnetic reconnection processes in three-dimensional (3D) complex field configurations have been investigated in different magneto-plasma systems in space, laboratory, and astrophysical systems. Two-dimensional (2D) features of magnetic reconnection have been well developed and applied successfully to systems with symmetrical property, such as toroidal fusion plasmas and laboratory experiments with an axial symmetry. But in asymmetric systems, the 3D features are inevitably different from those in the 2D case. Magnetic reconnection structures in multiple celestial body systems, particularly star–planet–Moon systems, bring fresh insights to the understanding of the 3D geometry of reconnection. Thus, we take magnetic reconnection in an ancient solar–lunar terrestrial magneto-plasma system as an example by using its crucial parameters approximately estimated already and also some specific applications in pathways for energy and matter transports among Earth, ancient Moon, and the interplanetary magnetic field (IMF). Then, magnetic reconnection of the ancient lunar–terrestrial magnetospheres with the IMF is investigated numerically in this work. In a 3D simulation for the Earth–Moon–IMF system, topological features of complex magnetic reconnection configurations and dynamical characteristics of magnetic reconnection processes are studied. It is found that a coupled lunar-terrestrial magnetosphere is formed, and under various IMF orientations, multiple X-points emerge at distinct locations, showing three typical magnetic reconnection structures in such a geometry, i.e., the X-line, the triple current sheets, and the A–B null pairs. The results can conduce to further understanding of reconnection physics in 3D for plasmas in complex magnetic configurations, and also a possible mechanism for energy and matters transport in evolutions of similar astrophysical systems.