A series of experiments were carried out to investigate polymer recovery in the micro hot embossing process. Above the glass transition temperature (Tg), polymer deformation becomes much easier and complete filling of microcavities is generally not difficult to achieve. One of the problems restricting replication efficiency of the hot embossing technique is polymer recovery. After complete filling, if without timely cooling, large recovery may happen and lead to defective embossing results. In this study, the recovery was found to be able to cause a height reduction of 21.4%, 17.8%, and 16.0% in the hot embossed micro-pyramid arrays, micro-pillar arrays, and micro-prism arrays respectively. This recovery can be avoided by means of prolonging embossing time or increasing embossing temperature. However, prolonging embossing time increases cycle time, while increasing embossing temperature is likely to induce severe warpage or damage problems. Thus, improvement of the embossing process is in urgent need. Through investigation on the recovery phenomena, which are characterized by that an apparent height and shape difference can be observed among adjacent embossed structures in the same polymer replica, it was found that interfacial bonding formed between the mold cavity wall and the polymer material is capable of preventing the recovery from happening. By applying the energy balanced approach widely used in fracture mechanics to the polymer recovery process, a theory of competition between the recovery and the adhesion was proposed, with which the experimental phenomena can be satisfactorily explained. During unloading, if the strain energy stored in the system for recovery is not enough for breaking the interfacial bonding, the recovery will be stopped; otherwise, large recovery may happen. To verify the theory, hot embossing experiments considering effects of process conditions and improved adhesion were conducted finally, further demonstrating that in the micrometer scale the adhesion has significant impacts on the recovery behavior of the polymer. Results of this research work indicate that we can take advantage of the adhesion to prevent the recovery and to achieve high-accuracy and high-efficiency micro hot embossing in the temperature range near the Tg.