Micro-milling is widely used in various crucial fields with the ability of machining micro- and meso-scaled functional structures on various materials efficiently. However, the micro-milling force model is not comprehensively developed yet when tool feature sizes continually decrease to under 200 µm in a low-stiffness system. This paper proposes an analytical force model considering the influence of tool radius, size effect, tool runout, tool deflection, and the actual trochoidal trajectories and the interaction of historical tool teeth trajectories (IHTTT). Different micro-milling status are recognized by analyzing the cutting process of different tool teeth. Conditions of single-tooth cutting status are determined by a proposed numerical algorithm, and entry angle and exit angle are analyzed under various cutting conditions for the low-stiffness system. Three micro-milling status, including single-tooth cutting status, are distinguished based on the instantaneous undeformed chip thickness resulting in three types of material removal mechanisms in predicting micro-milling force components. Discontinuous change rates of undeformed chip thickness are found in the low-stiffness micro-milling system. The proposed micro-milling force model is then verified through experiments of micro slot milling Elgiloy alloy with a 150-μm-diametrical two-teeth micro-end mill. The experimental results show a root-mean-square error (RSME) of 0.092 N in the predicted resultant force, accounting for approximately 5.12% of the measured force, by which the proposed theoretical model is verified to be of good prediction accuracy.