Although 3D point cloud data has received widespread attentions as a general form of 3D signal expression, applying point clouds to the task of dense correspondence estimation between 3D shapes has not been investigated widely. Furthermore, even in the few existing 3D point cloud-based methods, an important and widely acknowledged principle, i.e. one-toone matching, is usually ignored. In response, this paper presents a novel end-to-end learning-based method to estimate the dense correspondence of 3D point clouds, in which the problem of point matching is formulated as a zero-one assignment problem to achieve a permutation matching matrix to implement the oneto-one principle fundamentally. Note that the classical solutions of this assignment problem are always non-differentiable, which is fatal for deep learning frameworks. Thus we design a special matching module, which solves a doubly stochastic matrix at first and then projects this obtained approximate solution to the desired permutation matrix. Moreover, to guarantee end-to-end learning and the accuracy of the calculated loss, we calculate the loss from the learned permutation matrix but propagate the gradient to the doubly stochastic matrix directly which bypasses the permutation matrix during the backward propagation. Our method can be applied to both non-rigid and rigid 3D point cloud data and extensive experiments show that our method achieves state-of-the-art performance for dense correspondence learning.