The effects of fast neutron irradiation on oxygen atoms in Czochralski silicon (CZ-Si) are investigated systemically by using Fourier transform infrared (FTIR) spectrometer and positron annihilation technique (PAT). Through isochronal annealing, it is found that the trend of variation in interstitial oxygen concentration ([Oi]) in fast neutrons irradiated CZ-Si fluctuates largely with temperature increasing, especially between 500 and 700°C. After the CZ-Si is annealed at 600°C, the V4 appearing as three-dimensional vacancy clusters causes the formation of the molecule-like oxygen clusters, and more importantly these dimers with small binding energies (0.1–1.0eV) can diffuse into the Si lattices more easily than single oxygen atoms, thereby leading to the strong oxygen agglomerations. When the CZ-Si is annealed at temperature increasing up to 700°C, three-dimensional vacancy clusters disappear and the oxygen agglomerations decompose into single oxygen atoms (O) at interstitial sites. Results from FTIR spectrometer and PAT provide an insight into the nature of the [Oi] at temperatures between 500 and 700°C. It turns out that the large fluctuation of [Oi] after short-time annealing from 500 to 700°C results from the transformation of fast neutron irradiation defects.