With the development of microelectronics and flexible wearable electronic devices, poly(vinyl alcohol) (PVA) based thermal interface materials (TIMs) have received much attention. However, poor heat dissipation and high flammability have emerged as the key issues that restrict their application. In this work, the directional alignment of phytic acid (PA) modified boron nitride nanosheets (BNNS) and Ti3C2Tx MXene in PVA matrix was achieved by ice-templated assembly, which simultaneously enhanced the flame retardancy and thermal conductivity of PVA composite films (PVA/BTx). Owing to the synergistic effect between oriented BNNS and Ti3C2Tx MXene on forming the thermally conductive network within PVA matrix, the in-plane thermal conductivity of PVA/BTx-30 composite film was increased to 8.54 W m−1 K−1, much higher than that of PVA film (0.30 W m−1 K−1). Meanwhile, the heat dissipation process of PVA films applied as TIMs was simulated, which showed that PVA/BTx-30 films exhibited excellent thermal conduction and significantly decreased the operation temperature of electronic devices. Additionally, the peak heat release rate (PHRR) and total heat release (THR) of PVA/BTx-30 films were reduced by 60.3% and 62.0%, respectively, showing good flame retardancy. Importantly, the flexible Ti3C2Tx nanosheets further enhanced the mechanical properties of PVA/BTx composite films. Therefore, this work provides an effective method for the preparation of high thermal conductivity and flame retardant composite materials, which has important potential applications in the microelectronics industry.