The spontaneous parametric down-conversion source of entangled-photon pairs is important for applications in the quantum information process and quantum communication, but suffers from scattering by sample defect and air impurity. Here, we proposed an alternative scheme to manipulate the scattered SPDC process, where only a spatial light modulator was used to control the incident wavefront. The scheme was experimentally tested and also applied on the manipulation of photon pairs through the SPDC process with spectral control. This work proved the feasibility of manipulating nonlinear signals at quantum level with feedback-based wavefront shaping and also indicated applications in long-distance quantum key distribution, quantum communications, and quantum imaging, especially in complex environments.