The invention discloses core-shell structure thionazin composite microspheres and a preparation method thereof. The structural formula is shown by ASx@BPy, wherein 0.3<=x<=2, and 0.3<=y<=4. The method comprises the steps that firstly, powdery sulfide microspheres ASx are prepared, then, ASx powder, soluble salt of B and nontoxic red phosphorus are adopted as main raw materials, the core-shell structure thionazin composite microspheres are prepared by adopting a hydrothermal synthesis method under the effect of a surface active agent sodium dodecyl sulfonate (SDS), and the preparation method adopts nontoxic red phosphorus as a phosphorus source to replace a traditional raw material, namely, highly toxic, inflammable and explosive white phosphorus. The preparation method is simple and easy to implement, conditions are easy to control, the repeatability is good, and no later-period thermal treatment is needed. The prepared core-shell structure thionazin composite is better in catalytic performance compared with a single sulfide and phosphide, and can be used for lignin hydrogenation catalysis and photocatalytic degradation of dye wastewater.