In this work, polyamide 6 (PA6) composites with improved flame retardancy and thermal conductivity were prepared with different thermal conductive fillers (TC fillers) such as aluminum nitride (AlN) and boron nitride (BN) in a PA6 matrix with aluminum diethylphosphinate (AlPi) as a fire retardant. The resultant halogen-free flame retardant (HFFR) and thermal conductive (TC) PA6 (HFFR-TC-PA6) were investigated in detail with a mechanical property test, a limiting oxygen index (LOI), the vertical burning test (UL-94), a cone calorimeter, a thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The morphology of the impact fracture surface and char residue of the composites were analyzed by scanning electron microscopy (SEM). It was found that the thermal conductivity of the HFFR-TC-PA6 composite increased with the amount of TC fillers. The TC fillers exerted a positive effect for flame retardant PA6. For example, the HFFR-TC-PA6 composites with the thickness of 1.6 mm successfully passed the UL-94 V-0 rating with an LOI of more than 29% when the loading amount of AlN-550RFS, BN-SW08 and BN-NW04 was 30 wt%. The morphological structures of the char residues revealed that TC fillers formed a highly integrated char layer surface (without holes) during the combustion process, as compared to that of flame retardant PA6/AlPi composites. In addition, the thermal stability and crystallization behavior of the composites were studied.