With the aim of creating single‐ion Cu(II) spin qubits in a rigid metal–organic framework (MOF), this work demonstrates a doping of 5%, 2%, 1%, and 0.1% mol of Cu(II) ions into a perovskite‐type MOF [CH6N3][Zn(HCOO)3]. The presence of dopant Cu(II) sites are confirmed with anisotropic g‐factors (gx = 2.07, gy = 2.12, and gz = 2.44) in the S = 1/2 system by experimentally and theoretically. Magnetic dynamics indicate the occurrence of a slow magnetic relaxation via the direct and Raman processes under an applied field, with a relaxation time (τ) of 3.5 ms (5%Cu), 9.2 ms (2%Cu), and 15 ms (1%Cu) at 1.8 K. Furthermore, pulse‐ESR spectroscopy reveals spin qubit properties with a spin‐spin relaxation (phase memory) time (T2) of 0.21 μs (2%Cu), 0.39 μs (1%Cu), and 3.0 μs (0.1%Cu) at 10 K as well as Rabi oscillation between MS = ±1/2 spin sublevels. T2 above microsecond is achieved for the first time in the Cu(II)‐doped MOFs. It can be observed at submicrosecond around 50 K. These spin relaxations are very sensitive to the spin–spin interactions relating with cross‐relaxation between the Cu(II) sites and can be tuned by adjusting the dopant concentration.