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We propose a new approach to explore CPT violation of neutrino oscillations through a fluctuating matter based on time-dependent geometric quantities. By mapping the neutrino oscillations onto a Poincaré sphere structure, we obtain an analytic solution of master equation and further define the geometric quantities, i.e., radius of Poincaré sphere and geometric phase. We find that the mixing process between electron and muon neutrinos can be described by the radius of Poincaré sphere that depends on the intrinsic CP-violating angle. Such a radius reveals a dynamic mechanism of CPT-violation, i.e., both spontaneous symmetry breaking and Majorana–Dirac neutrino confusion. We show that the time-dependent geometric phase can be used to find the neutrino nature and observe the CPT-violation because it is strongly enhanced under the neutrino propagation. We further show that the time-dependent geometric phase can be easily detected by simulating the neutrino oscillation based on fluctuating magnetic fields in nuclear magnetic resonance, which makes the experimental observation of CPT-violation possible in the neutrino mixing and oscillations.