The species was reported as new to science in 2006 by Shu-Hong Li and colleagues from the Yunnan Agricultural University.

The specific epithet deqinensis refers to Dêqên County in Yunnan, where the type specimen was collected.

The intersection of vertical and horizontal ridges form irregularly shaped, cream-coloured pits that are generally two or three times as long as they are wide.

[1] Morchella umbrina is somewhat similar in appearance to M. deqinensis, but the former species can be distinguished by its deeper colour, the smaller pits on the cap surface, and the absence of granules on the stipe.

[1] Morchella deqinensis is known only from China, where it fruits on the ground in coniferous and mixed forests at an elevation of 2,800–3,200 m (9,200–10,500 ft).