Combining synthetic polymer scaffolds with inorganic bioactive factors is widely used to promote the bioactivity and bone conductivity of bone tissue. However, except for the chemical composition of scaffold, the biomimetic structure also plays an important role in its application. In this study, we report the fabrication of polylactic acid/hydroxyapatite (PLA/HA) composite nanofibrous scaffolds via phase separation method to mimic the native extracellular matrix (ECM). The SEM analysis showed that the addition of HA dramatically impacted the morphology of the PLA matrix, which changed from 3D nanofibrous network structure to a disorderly micro-nanofibrous porous structure. At the same time, HA particles could be evenly dispersed at the end of the fiber. The FTIR and XRD demonstrated that there was not any chemical interaction between PLA and HA. Thermal analyses showed that HA could decrease the crystallization of PLA, but improve the thermal decomposition temperature of the composite scaffold. Moreover, water contact angle analysis of the PLA/HA composite scaffold demonstrated that the hydrophilicity increased with the addition of HA. Furthermore, apatite-formation ability tests confirmed that HA could not only more and faster induced the deposition of weak hydroxyapatite but also induced specific morphology of HA.