A micro-electro-mechanical systems (MEMS) terminal structure of board-to-board electrical connector and manufacturing method thereof are provided. The terminal of the terminal structure includes a side arm, a bent portion, and a flexible arm integrally formed as one component. The flexible arm includes a first portion and a second portion. The first portion and the side arm form an insertion space. The second portion and the side arm form a locking space. The second portion of the flexible arm has a contact portion. The insertion space is greater than the locking space. The terminal has curved and locking features to extend the moment arm of the terminal for improving the terminal flexibility. The terminal contacts a mating terminal through multiple points, thereby improving the contact stability and providing the locking function. Furthermore, by using the MEMS techniques for semiconductor industries, the terminal of micro board-to-board electrical connector can be manufactured.