In this article, the hyperspectral unmixing problem is solved with the nonnegative matrix factorization (NMF) algorithm. The regularized criterion is minimized with a hierarchical alternating least squares (HALS) scheme. Under the HALS framework, four constraints are introduced to improve the unmixing accuracy, including the sum-to-unity constraint, the constraints for minimum spectral dispersion and maximum spatial dispersion, and the minimum volume constraint. The derived algorithm is called F-NMF, for NMF with flexible constraints. We experimentally compare F-NMF with different constraints and combined ones. We test the sensitivity and robustness of F-NMF to many parameters such as the purity level of endmembers, the number of endmembers and pixels, the SNR, the sparsity level of abundances, and the overestimation of endmembers. The proposed algorithm improves the results estimated by vertex component analysis. A comparative analysis on real data is included. The unmixing results given by a geometrical method, the simplex identification via split augmented Lagrangian and the F-NMF algorithms with combined constraints are compared, which shows the relative stability of F-NMF.