Absolute chiral environments are rare in regular polyhedral and prismatic architectures, but are achievable from self-assembly of metal-organic cages/containers (MOCs), which endow us with a promising ability to imitate natural organization systems to accomplish stereochemical recognition, catalysis and separation. Here we report a general assembly approach to homochiral MOCs with robust chemical viability suitable for various practical applications. A stepwise process for assembly of enantiopure ΔΔΔΔΔΔΔΔ- and ΛΛΛΛΛΛΛΛ-Pd6(RuL3)8 MOCs is accomplished by pre-resolution of the Δ/Λ-Ru-metalloligand precursors. The obtained Pd-Ru bimetallic MOCs feature in large D4-symmetric chiral space imposed by the predetermined Ru(II)-octahedral stereoconfigurations, which are substitutionally inert, stable, water-soluble and are capable of encapsulating a dozen guests per cage. Chiral resolution tests reveal diverse host-guest stereoselectivity towards different chiral molecules, which demonstrate enantioseparation ability for atropisomeric compounds with C2 symmetry. NMR studies indicate a distinctive resolution process depending on guest exchange dynamics, which is differentiable between host-guest diastereomers.