Study and application of MIL-100(Fe)-based two-dimensional graphene oxide (GO) nanocomposite was limited because the nucleation of the spherical structure of MIL-100(Fe) on GO along different directions hindered the formation of MOF-100(Fe). To address this issue, MIL-100(Fe)/three-dimensional graphene (3DG) nanocomposites (abbreviated as MIL-3DG-n, n = 25, 50, 75, and 100) were successfully fabricated via in situ growth of MIL-100(Fe) on 3DG matrixes in this work because the unique structure of 3DG can avoid the attachment with MIL-100(Fe) on nucleation sites along multiple directions, resulting in their ideal combination. The prepared MIL-3DG nanocomposites exhibited higher peroxidase-like catalytic activities than pure MIL-100(Fe), and MIL-3DG-75 exhibited the best peroxidase-like activities for detecting xanthine with the detection limit of 0.0014 μM in the linear range of 0–200 μM to date, to the best of our knowledge, which is attributed to the higher affinity of MIL-3DG-75 nanocomposite to peroxidase substrates o-phenylenediamine (OPD) and H2O2, confirmed by the Michaelis–Menten kinetics (Vm: 49.5 × 10–8 M s–1 for H2O2, 18 × 10–8 M s–1 for OPD, Km: 0.029 mM for H2O2, 0.011 mM for OPD). Owing to the high catalytic efficiency of the MIL-3DG-75 nanocomposite, a rapid and efficient strategy for the sensitive colorimetric detection of xanthine was established.