The invention relates to a composite nanoparticle with a Janus structure and a preparation method and application thereof. Specifically, the particle has a structure shown as a formula I and a formula II, in the formulas, X represents an oxide particle of transition metal A, Y represents an oxide particle of transition metal B, Z represents an oxide particle of transition metal C, and the particle has the characteristic of producing a magnetic resonance imaging weighting signal. When the transition metal is Mn, a transition metal oxide is Mn3O4. The invention further discloses the preparation method and application of the particle. The particle is applied to the weighting MRI process, a clearer imaging effect and higher sensitivity than flat scanning can be obtained, and the treatment process can also be visually monitored in real time.