Construction of high performance flame-retardant engineering plastics is of particular interest both in academia and industrial circles for years. Herein, a novel organic-inorganic hybrid (BM@Al-BuPPi) with unique core-shell structure was prepared based on the reaction of isobutyl-phenylphosphinic acid (Bu-PPiA) and boehmite (BM) via analogue suspension in aqueous solution. The core from the self-aggregated microrod of Al-BuPPi brought a high flame-retardant efficiency to the hybrid, where the V-0 rating in UL-94 burning test and 42.5% of limiting oxygen index (LOI) were achieved. The shell composed of BM nanoparticles was responsible for the improvement of the compatibility between hybrid and semi-aromatic polyamide matrix by increasing the surface polarity and the wettability of the hybrid. Compared with the original Al-BuPPi, the hybrid was homogeneously wrapped by the matrix, and the tensile strength of semi-aromatic polyamide/hybrid composite was over twice higher than that of the flame-retardant composite containing Al-BuPPi. At last, cone calorimetric results revealed the hybrid combines both advantages of the organic phosphinate and the inorganic boehmite in flame inhibition and smoke suppressing activity.