An isothermally hot-embossing methodology was proposed for the flattening of plastic microreactors. The flattening principles of a plane plastic microreactor by the isothermally hot-embossing methodology were researched and an elastic-plastic model was established to describe the deformation process. The influences of temperature and pressure on the topography of plastic microparts were quantitatively analyzed. By considering the flattening effect and microstructure of the plastic microreactor, the effect of main technological parameters on the flattening accuracy was analyzed by the isothermally hot-embossing methodology. The result indicates that the influence of thermal load on flattening degree is more obvious than that of the external pressure. The deformations at the ends of microreactor are much larger than that of the middle chamber owing to the larger contact area at the ends. The changing rates of flatness and waviness come to the maximum value when the temperature is 70 ℃ at the same pressure. After optimization, the changing rate of flatness achieves to 72.7% and the flatness of the microreactor is improved within 10 μm by the hot embossing technology. Moreover, the changing rate of waviness ranges from 3.50% to 53.5% at different regions of plastic microparts and the deformation of the microstructure size is controlled within 5 μm. The study is beneficial to improrement of the precision of flat plastic microparts.