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Precise manipulation of the time–frequency modes of entangled photons is crucial for future quantum science and technologies. Recently, the frequency-domain-quantum-optical-synthesis (FD-QOS) method was demonstrated by creating a superposition of different joint temporal amplitudes: those temporal distributions can be controlled by manipulating the joint spectral amplitude in 2D frequency space via a Fourier optical relation. This FD-QOS method provides an efficient, flexible, and easy-to-control way to precisely modulate the temporal distributions of the entangled photon in an ultrafast region. However, manipulation of only the temporal modes is not sufficient for various applications in quantum information, since spectral modulations are also needed on many occasions. Here, we present a proof-of-concept experiment of two-photon spectral modulation via temporal manipulation of a biphoton wave packet. This protocol, called time-domain-quantum-optical-synthesis (TD-QOS), is achieved by adjusting the relative phases between two joint temporal distributions. In addition, the two-photon joint spectral distributions are characterized by measuring the joint spectral intensities and Hong–Ou–Mandel interferences. The combination of FD-QOS and TD-QOS enables complete control over the biphoton states. Our work would further develop quantum technologies that rely on the time–frequency modes of entangled photons.