Abstract: The Pancharatnam phase of deformed Jaynes-Cummings(J-C) model was obtained analytically. The evolution of Pancharatnam phase for deformed Jaynes-Cummings model, was also discussed. The difference between the Pancharatnam phase evolution for deformed J-C model and that of conventional J-C model has been investigated. The results show that the Pancharatnam phase reveals some information of population reversion of an atom and the quantum nature of the cavity field. And the larger is the average photon number，the larger is the difference of Pancharatnam phase evolution between deformed J-C model and conventional J-C model. This exhibits that the evolution of Pancharatnam phase is closely relative to the quantum algebra structure of the system.