Here, we report the scalable fabrication of 2i-functionalized micro-pyramid-array (μPyA/+2i) inserts for use in commercial multi-well plates, as the alternative cultivation platform for maintaining long-term self-renewal and pluripotency of multiple mESCs and mouse induced pluripotent stem cells. Relevant evidence including cell morphology characterization increased alkaline phosphatase activity, high expression of mESC self-renewal markers, decreased levels of differentiation-associated markers, and high proportion of self-renewal marker cells are provided. Further studies demonstrated that μPyA/+2i could cause a higher cell density in mESC colony, and induce gene expression changes. Subsequent studies showed that μPyA/+2i can influence the cytoskeleton and promote cell adhesion through upregulation. In summary, these μPyA/+2i inserts offer flexible and gelatin-free micro-envriomnets to maintain long-term self-renewal and pluripotency of mESCs. Enabled by the microstructured inserst, the facile stem cell manipulation and transfer among culture dishes will broaden stem cells both in routine and translational applications.