A novel halogen‐free flame retardant copolyamide 6,6 (FR‐PA66) was prepared successfully by in situ polymerizing with adipic acid hexamethylene salt and 2‐carboxy ethyl (phenyl) phosphinic acid (CEPPA). The elemental composition and chemical structure of FR‐PA66 were characterized by energy dispersive X‐ray spectroscopy, Fourier transform infrared spectrometer and 13C Nuclear magnetic resonance spectrometer. The flame retardancy, thermal stability, and morphology of char residues were also investigated by the limiting oxygen index (LOI), UL 94 test, thermogravimetric analysis, and scanning electron microscopy. The results showed that FR‐PA66 samples had much better flame retardancy and char formation ability than pure PA66 after the flame retardant modification. The LOI values were increased from 24.0 to 28.0% by adding 6 wt % of CEPPA and all FR‐PA66 samples were rated as V‐0 rating in UL‐94 test. Furthermore, the thermal stability analysis indicated that in situ polymerization with CEPPA effectively decreased the initial decomposition temperature and increased the amount of char residue. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 137, 48687.