A template-free solvothermal combined with precursor thermal transformation method has been developed for the preparation of flower-like Fe₃O₄ nanostructured hollow microspheres. The reaction mechanism and the self-assembly evolution process were studied, and it was found that the synthetic conditions for the precursor such as reaction time, urea concentration and non-aqueous media are all crucial for the formation of the flower-like hierarchical precursors. The flower-like Fe₃O₄ microspheres obtained by calcining the precursor in Ar gas exhibit superparamagnetic behavior and show relative high saturation magnetization at room temperature. To endow them with SERS activity, silver coating was conducted by magnetron sputtering. The obtained Fe₃O₄/Ag hybrid microflowers make a positive influence on the high sensitivity of SERS to 4-pyridinethiol (4-Mpy) and Rhodamine 6G (R6G) molecules when compared with the silver film substrates. More importantly, the detection limit of Fe₃O₄/Ag hybrid microflowers for R6G dye can reach up to 10⁻¹⁵ M, which meets the requirements of ultratrace detection of analytes using SERS. Thus, the SERS-active magnetic hybrids prepared in this work may possibly be used as an optical probe with magnetic function for application in high-sensitivity bioassays.