In this work, we experimentally manipulate the spectrum and phase of a biphoton wave packet in a two-dimensional frequency space. The spectrum is shaped by adjusting the temperature of the crystal, and the phase is controlled by tilting the dispersive glass plate. The manipulating effects are confirmed by measuring the two-photon spectral intensity (TSI) and the Hong-Ou-Mandel (HOM) interference patterns. Unlike the previous independent manipulation schemes, here we perform joint manipulation on the biphoton spectrum. The technique in this work paves the way for arbitrary shaping of a multi-photon wave packet in a quantum manner.