Low-symmetry metal–organic cages (MOCs) have received increasing attention due to their complex structures and more advanced functions. Here, we report a new MOC cage with a unique trigonal bipyramidal configuration, [M₅L₆], constructed via the combination effects of coordination bonds and π⋯π interactions. A series of structures (BIF-136 to BIF-141) based on this [M₅L₆] cage were synthesized by the self-assembly of BH(bim)₃⁻ ligands and Ni(II) ions under various solvothermal conditions. Each [M₅L₆] consists of two [M₄L₃] defective cubic cages sharing three metal nodes, which include two geometric types of flexible Ni(II) centers (tetrahedral and octahedral). Benefiting from these modifiable metal centers, these cage-based crystals realized abundant coordination environments and a dimension transition from a 0D cage to a 1D cage-based chain, accompanied by modulations of conjugation degrees, electronic push–pull effects and band gaps. Due to their diverse structural features, we have systematically investigated their third-order nonlinear optical (NLO) properties. To our surprise, these structures show a typical reverse saturated absorption (RSA) response. In particular, BIF-141 achieves excellent optical limiting (OL) performance with a low minimum normalized transmittance (T_min) of 0.20. This study not only provides a new strategy for constructing low-symmetry cages but also contributes to the understanding of the mechanism of their optical applications.