Abstract It is NP-complete to find non-negative factors W and H with fixed rank r from a non-negative matrix X by minimizing kX ? W H > k2F . Although the separability assumption (all data points are in the conical hull of the extreme rows) enables polynomial-time algorithms, the computational cost is not affordable for big data. This paper investigates how the power of quantum computation can be capitalized to solve the non-negative matrix factorization with the separability assumption (SNMF) by devising a quantum algorithm based on the divide-and-conquer anchoring (DCA) scheme [Zhou et al., 2013]. The design of quantum DCA (QDCA) is challenging. In the divide step, the random projections in DCA is completed by a quantum algorithm for linear operations, which achieves the exponential speedup. We then devise a heuristic post-selection procedure which extracts the information of anchors stored in the quantum states efficiently. Under a plausible assumption, QDCA performs efficiently, achieves the quantum speedup, and is beneficial for high dimensional problems.