The invention discloses a modified charcoal microballoon, and a preparation method and an application thereof. The preparation method for the modified charcoal microballoon comprises the following steps: (1) taking thalia dealbata powder, soaking in a soluble magnesium salt solution, filtering, taking out and then drying, thereby obtaining magnesium modified thalia dealbata powder; (2) carbonizing the thalia dealbata powder, thereby obtaining the modified charcoal; (3) taking the modified charcoal, and by taking a sodium alginate solution as an embedding medium and CaCl2 solution as a cross-linking agent, performing gel embedding and drying after embedding, thereby acquiring the modified charcoal microballoon. According to invention, the thalia dealbata powder is modified with magnesium at first, and then the modified thalia dealbata powder is taken as a precursor for carbonization, and lastly, the sodium alga acid solution is taken as the embedding medium for preparing the modified charcoal into microballoon; the obtained modified charcoal microballoon can effectively remove phosphorus from water and the removal rate is high; the abandoned thalia dealbata is recycled, so that the resource utilization of the wastes is realized.