Aligned submicron fibers have played an essential role in inducing stem cell proliferation and differentiation in tissue engineering. However, it remains challenging to fully understand and modify the differences between stem cell proliferation and differentiation on aligned-random fibers. Therefore, in this study, we aimed to identify the differential causes of stem cell proliferation and differentiation between BMSCs on aligned-random fibers with different elastic modulus, and to change the differential levels between them through a regulatory mechanism mediated by BCL-6 and miR-126-5p. The results showed that the most significant PIP2 alterations were found in the aligned fibers compared with the random fibers, which had a regular and oriented structure, excellent elastic modulus and cytocompatibility, regular cytoskeleton and movement pattern, high differentiation potential, and the most differentiated PIP2 gene. The same trend was actual for the aligned fibers with a lower elastic modulus. The level of proliferative differentiation genes in cells on random fibers and high elastic modulus aligned fibers was altered by BCL-6 and miR-126-5p mediated regulatory mechanisms to make the apparent cell distribution nearly consistent with the cell state on low elastic modulus aligned fibers. This work demonstrates the reason for the difference of cells between the two kinds of fibers and on fibers with different elastic modulus. It provides more insights for understanding the gene-level regulation of cell growth in tissue engineering. These findings will greatly help the application and design of 3D tissue culture for tissue engineering. This article is protected by copyright. All rights reserved.