In this work, small amounts of piperazine/phenyl-silicon charring skeleton NSi-n (n=1, 2, 3) with varied aggregation degrees were respectively inserted into a hydrogen-bonded macromolecule fabricated with melamine and cyanuric acid, to prepare a series of nitrogen/silicon-based macromolecules MNSi-n (n=1, 2, 3), which achieved the efficient charring flame retardant effect of MNSi-n/ammonium polyphosphate (APP) in polypropylene (PP). Due to the formation of compact barrier char layers with rich phosphorus and silicon contents, (MNSi-n/APP)/PP performed higher limited oxygen index, glow-wire flammable index and UL 94 V-0 level, and also exhibited lower heat release rate. Comparatively, the melamine cyanurate macromolecule without NSi-n skeleton with APP only formed ineffective char layers and weaker flame retardancy. More importantly, the higher aggregation degree of piperazine and phenyl-silicon groups in MNSi-n apparently led to higher intumescent flame retardant efficiency. The high aggregation degree of NSi-n structure strengthened the full interaction between macromolecules MNSi-n and APP, thus forming compact char layers and increasing flame retardancy. It disclosed an effective way to enhance charring flame retardancy by small changes in molecular structure.