With the exploration of the World Wide Web, more and more entities are involved in various online applications, e.g., recommender systems and social network services. In such context, high-dimensional sparse matrices describing the relationships among them are frequently encountered. It is highly important to develop efficient non-negative latent factor (NLF) models for these high-dimensional sparse relationships because of a) their ability to extract useful knowledge from them; b) their fulfillment of the non-negativity constraints for representing most non-negative industrial data; and c) their high computational and storage efficiency on high-dimensional sparse matrices. However, due to the imbalanced distribution of known data in such a matrix, it is necessary to investigate the regularization effect in NLF models. We first review the NLF model briefly. Then we propose to integrate the frequency-weight on each involved entity into its Tikhonov regularization terms, for representing the imbalanced data from a high-dimensional sparse matrix. Experimental results on industrial-size matrices indicate that the proposed scheme is effective in improving the performance of the NLF model in missing-data-estimation.