Three heterometallic Fe₆Ln₄ clusters were self-assembled by using N-methyldiethanolamine (H₂mdea) and 3,5-dinitrobenzoic acid (Hdnbz) as principal building blocks and azide as an ancillary ligand. The obtained products 1–3 were isolated as air-stable microcrystalline solids and fully characterized. Single-crystal X-ray diffraction studies reveal similar type of molecular units [Fe₆Ln₄(μ₄-O)₂(μ₃-OH)₂(mdea)₆(dnbz)₈(N₃)₄]·2MeCN·xH₂O·CH₂Cl₂ {Ln = Y (1), Gd (2), Dy (3); x = 4, 6, 10, respectively}. Topological analysis of 1–3 was performed following a method for high nuclearity coordination clusters. The [Fe₆Ln₄(μ-O)₁₀(μ₃-O)₄(μ₄-O)₂] cores were identified in all structures and further simplified to graph topological skeletons, which were classified as pentanodal 2,3,3,5,6-connected motifs with the unique topology. The magnetic behavior of 1–3 was investigated in detail. The magnetic studies and magnetocaloric measurements reveal that the tetranuclear gadolinium centers of 2 exhibit a high cryogenic magnetocaloric effect (MCE) that reaches 13.66 J·kg^–1·K^–1 (25.18 mJ·cm^–3·K^–1) for ΔH = 90 kOe at 4.5 K. Among all the compounds, only 3 shows the ac-signals (ac, alternating current) and slow-relaxation behavior, which is a peculiar characteristic of a single-molecule magnet (SMM), giving a value of U_eff = 19.5(4) K. The present work thus contributes to the design of topologically unique discrete crystalline materials with notable functional properties.