Because of phase compensation instability (PCI), the thermal blooming phase compensation issue is more and more concerned. The frequency-weighted deformable mirror (DM) eigen modes are generated by orthogonalizing the coupling matrix between DM actuator influence functions. The numerical model of wave-front reconstruction algorithm based on DM eigen mode is established, and the adaptive optical (AO) system based on this wave-front reconstruction algorithm for correcting thermal bloomed wave-front is numerically simulated. Results show that compared to the direct slop method, the DM eigen mode reconstruction method can change the spatial frequency of correction phase through eigen mode chosen, eliminate the effect of high spatial frequency on thermal blooming correction, stabilize the AO system close loop control, and improve the system correction thermal blooming performance.