Biphotons of narrow bandwidth and long temporal length play a crucial role in long-distance quantum communication (LDQC) and linear optical quantum computing (LOQC). However, generation of these photons usually requires atomic ensembles with high optical depth or spontaneous parametric down-conversion with sophisticated optical cavity. By manipulating the two-component biphoton wavefunction generated from a low-optical-depth (low-OD) atomic ensemble, we demonstrate biphotons with subnatural linewidth in the sub-MHz regime. The potential of shaping and manipulating the quantum wavepackets of these temporally long photons is also demonstrated and discussed. Our work has potential applications in realizing quantum repeaters and large cluster states for LDQC and LOQC, respectively. The possibility to generate and manipulate subnatural-linewidth biphotons with low OD also opens up new opportunity to miniaturize the biphoton source for implementing quantum technologies on chip-scale quantum devices.