The unclear assembly mechanism seriously hinders the preparation and application of 3d-4f heterometallic clusters. Two new heterometallic nanoclusters [Dy2Mn4(HL)4(OAc)6]·5EtOH·H2O (1) and [Gd2Mn4(HL)4(OAc)6]·4EtOH·4H2O (2) were obtained from the in situ condensation reaction of 3-amino-1,2-propanediol with 2-hydroxy-1-naphthaldehyde. The intermediate species in the cluster 1 synthesis process were tracked by time-dependent high-resolution electrospray ionization mass spectrometry (HRESI-MS), further revealing the possible formation mechanism (Dy → DyL2 →DyMn2L2 → DyMn3L2 → DyMn4L3 → Dy2Mn4L4). Magnetic studies indicated that the antiferromagnet LnIII-MnII (Ln = DyIII and GdIII) interaction was operative in both titled clusters. Furthermore, the performance of the clusters was regulated by adjusting the type of rare earth ions (DyIII and GdIII). The research results showed that cluster 2 containing GdIII exhibited an excellent longitudinal relaxation rate (r1) with 1.95 mM-1 s-1 under 0.5 T and a relatively suitable r2/r1 value (3.88), which indicated that it can be used as a new and efficient T1 MR contrast agent. Cluster 1 containing DyIII displayed antipathogenic activities against clinical MRSA strain with an MIC of 32 μg/mL. This work not only provided a reference for revealing the assembly mechanism of 3d-4f heterometallic clusters but also confirmed its potential application in the biomedical field.