To control the dissolution process of a phosphorous-containing poly(arylene ether ketone) (P-PAEK)/bismaleimide (BMI) resin diphase system, a series of P-PAEKs were synthesized by changing the molar ratio of the reactants through nucleophilic substitution. The U3160/BMI composites toughened with P-PAEK film were manufactured by resin transfer moulding based on the concept of ex situ toughening. In addition, the interlaminar properties of the composites were characterized by applying modes I and II fracture toughness tests. The mode I fracture toughness of the composite was shown to be less improved, whereas the mode II fracture toughness was increased by about 74%. Furthermore, the interlaminar microstructure, which was observed by using a scanning electron microscope (SEM), revealed that reaction-induced phase decomposition and inversion occurred in the interlaminar region. The improvement in fracture toughness was attributed to plastic rupture of the continuous P-PAEK phase and debonding or cavitations of the BMI particle phases. Through the application of ex situ toughening, the compression-after-impact properties of the composite were significantly improved, whereas the thermodynamic properties were well maintained. Besides, optical microscopy images showed more space in the interlayer of the toughened specimens, which contributed to the improvement of damage tolerance.