During micro-milling aluminum alloy LF21 process, it tends to produce large top burr usually detected at the top of slot walls. Therefore, the machining accuracy and quality of the micro-parts are difficult to satisfy. To suppress burr and achieve the higher machining quality of machined LF21 micro-parts, this paper using the Johnson–Cook constitutive model establishes a two-dimensional finite element simulation model to obtain a better recognition of burr formation mechanisms and a three-dimensional finite element simulation model to better simulate burr formation process and measure top burr height. Furthermore, effective validation experiments for the proposed models are conducted, good agreements are achieved in the cutting force and top burr height between the experiments and simulation results. The study explores the formation mechanism of top burr in micro-milling LF21 and reveals the influence law of cutting parameters on top burr height based on the simulation and experimental results. The research guides the selection of cutting parameters in micro-milling LF21 process.