AbstractIn this paper, a dynamic temperature compensation method is presented to stabilize the wavelength of the entangled biphoton source, which is generated on spontaneous parametric down‐conversion from a magnesium oxide doped periodically poled lithium niobate waveguide. Utilizing the dispersive Fourier transformation technique, the photon wavelength variation is monitored in case of conventional static temperature control, revealing a long‐term wavelength drift up to 556.8 pm over a 14‐h measurement period. A Hong‐Ou‐Mandel (HOM) interferometer is constructed to assess the impact on quantum applications, showing a decrease in visibility from 95.5% to 69.4%. To address this issue, a digital proportional‐integral‐differential algorithm is implemented to dynamically compensate the working temperature variation of the waveguide, thereby instantly stabilizing the wavelength to a peak‐to‐peak fluctuation of +138.05 pm/‐127.61 pm with the standard deviation being 30.49 pm. The wavelength stability shows more than a hundredfold enhancement in terms of Allan deviation, reaching at an averaging time of 10000 s. With the dynamic control in operation, the HOM interference visibility turns to stable at 96.1% ± 0.6%. The method provides a simple and accessible solution for precisely controlling and stabilizing the wavelength of entangled biphotons, thus improving performance in various quantum information processing applications.