Quantum interference plays an essential role in understanding the concepts of quantum physics. Moreover, the interference of photons is indispensable for large-scale quantum information processing. With the development of quantum networks, interference of photons transmitted through long-distance fiber channels has been widely implemented. However, quantum interference of photons using free-space channels is still scarce, mainly due to atmospheric turbulence. Here, we report an experimental demonstration of Hong-Ou-Mandel interference with photons transmitted by free-space channels. Two typical photon sources, i.e., correlated photon pairs generated in spontaneous parametric down conversion (SPDC) process and weak coherent states, are employed. A visibility of 0.744 ± 0.013 is observed by interfering with two photons generated in the SPDC process, exceeding the classical limit of 0.5. Our results demonstrate that the quantum property of photons remains even after transmission through unstable free-space channels, indicating the feasibility and potential application of free-space-based quantum interference in quantum information processing.