The invention discloses a new process for preparing modified melamine polyphosphate, which comprises the following steps: (1) adding water, phosphoric acid and a modifier into a reaction kettle, and heating to 20-70 DEG C; (2) adding melamine, heating to 90-100 DEG C, and reacting for 2-5 hours; (3) cooling the product obtained after the reaction in the step (2), filtering, and drying; and (4) carrying out polymerization reaction on the product, which is subjected to the step (3), at 300-450 DEG C for 10-120 minutes. The synthesis and modification of the melamine polyphosphate are carried out synchronously, so that the invention has the advantages of short reaction time, low requirements for raw materials, simple and convenient technical operation, and low environmental pollution; the prepared melamine polyphosphate has the advantages of favorable compatibility with resin, low solubility in water, and excellent thermal stability, and the temperature can reach about 360 DEG C when the weight loss is 2%, so that the modified melamine polyphosphate can satisfy the processing requirements of no halogen and flame retardancy for glass fiber reinforced nylon and polyester.