The integration of advanced diagnostic contrast agents with versatile therapeutic drugs is an effective method for cancer treatment. However, combining various biocompatible theranostic modalities into a single platform at the nanoscale is a challenging assignment. In this work, we report a simple chemical synthetic route for producing a homogeneous hybrid nanoflower shaped morphology based on Au@Mn3O4 magneto-plasmonic nanomaterials. The synthetic mechanism of the nanoflowers is well-matched with the heteroepitaxial growth phenomena by which the nano-petals of Mn3O4 generated on the surface of the Au core. The food and drug administration (FDA) in the USA approved the use of triblock polymer Pluronic F-127 to enhance the biocompatibility of Au@Mn3O4 hybrid nanoflowers. The prepared hybrid nanoflowers produce a significant photothermal heating effect with a thermal transduction efficiency of 38%, comparable to the nanorods and nanoparticles of gold (Au). The hybrid junction reveals promising optical and magnetic properties and the prepared Au@Mn3O4 nanoflowers not only exhibit strong near-infrared (NIR) absorption to produce excellent photothermal efficacy under irradiation with an 808 nm NIR laser, but also demonstrate a significant T1-weighted magnetic resonance (MR) image enhancement in vitro and in vivo. The histopathology assessments indicate only negligible toxicity of the nanoflowers to major organs. Therefore, the hybrid Au@Mn3O4 nanoflowers exhibit great potential in T1-weighted MR-imaging and photothermal therapy, opening up new possibilities for synthesizing novel bio-compatible, homogeneous, and shape controllable nanostructures with multifunctional applications.