The flattening filter free (FFF) X‐rays can provide much higher dose rate at the treatment target compared to the conventional flattened X‐rays. However, the substantial increase of dose rate for FFF beams may affect the ion recombination correction factor, which is required for accurate measurements using ionization chambers in clinical dosimetry. The purpose of this work is to investigate the ion recombination of three types of commonly used ion chambers (Farmer, PinPoint and plane‐parallel) in the FFF photon radiation. Both 6 MV and 10 MV flattened and FFF beams were fully commissioned on a Varian TrueBeam linear accelerator. The ion recombination correction factor, normalPion, was determined using the two‐voltage technique for a 0.6 cc Farmer chamber, a 0.015 cc PinPoint chamber, and a 0.02 cc parallel‐plate chamber at different source‐to‐axis distances (SAD) in a solid water phantom or water tank phantom at a depth of 10 cm in a 10×10 cm2 field. Good repeatability of measurements was demonstrated. Less than 1% difference in Pion between the flattened and FFF photons for all three ion chambers was observed. At a SAD of 100 cm and a depth of 10 cm for a 10×10 cm2 field, normalPion for the Farmer chamber was 1.004 and 1.008 for the 6 MV flattened and FFF beams, respectively. At the same setup using the Farmer chamber, normalPion was 1.002 and 1.015 for the 10 MV flattened and FFF beams, respectively. All normalPion results for the Farmer, PinPoint, or parallel plate chamber in the 6 MV and 10 MV flattened and FFF beams were within 2% from the unity (1 ≤ normalPion < 1.02). The normalPion ratio of the FFF to flattened beams was 0.99~1.01 for both 6 MV and 10 MV photons. The ion recombination effect of the Farmer, PinPoint, and plane‐parallel chamber in the FFF beams is not substantially different from that in the conventional flattened beams.PACS number: 87.56.bd