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In this paper we combine simple genetic algorithm (SGA) with simulated annealing (SA) and propose a new niche genetic simulated annealing algorithm (NGSAA) to invert reservoir parameters (including porosity, solid phase density and fluid phase density) in a two-phase fractured medium. The SGA integrates the SA idea, and niche technology is introduced to maintain population diversity. NGSAA has the global searching ability of SGA together with the local fast converging ability of SA. We take the two-phase fractured medium of the BISQ model in a two-dimensional half space as an example, and carry out the numerical reservoir parameters inversion experiments. Then we provide the comparison between NGSAA results and SGA results. The experiments show that the stability, calculation accuracy and solving efficiency of NGSAA are all higher than that of SGA. So the NGSAA is an effective method to invert reservoir parameters in a two-phase fractured medium.