The indistinguishability of independent single photons is presented by decomposing the single photon pulse into the mixed state of different transform limited pulses. The entanglement between single photons and outer environment or other photons induces the distribution of the center frequencies of those transform limited pulses and makes photons distinguishable. Only the single photons with the same transform limited form are indistinguishable. In details, the indistinguishability of single photons from the solid-state quantum emitter and spontaneous parametric down conversion is examined with two-photon Hong-Ou-Mandel interferometer. Moreover, experimental methods to enhance the indistinguishability are discussed, where the usage of spectral filter is highlighted.