The carbonate reservoirs in the Tarim Basin are characterized by low matrix-porosity, heterogeneity and anisotropy, which make it difficult to predict and evaluate these reservoirs. The reservoir formations in Lundong area experienced a series of diagenesis and tectonic evolution stages. And secondary storage spaces such as fractures and dissolution caves were developed while nearly all the primary pores have disappeared. Based on a summary of different types of storage spaces and their responses in conventional logs, FMI and full waveform sonic logs which are sensitive to different reservoirs, the comprehensive probability index (CPI) method is applied to evaluating the reservoirs and a standard of reservoir classifi cation is established. By comparing the evaluation results with actual welllogging results, the method has proven to be practical for formation evaluation of carbonate reservoirs, especially for the fractured carbonate reservoirs. In reservoir fluid identification, the multivariate stepwise discriminant analysis (MSDA) method is introduced. Combining the CPI method and MSDA method, comprehensive formation evaluation has been performed for fractured and caved carbonate reservoirs in the Tarim Basin. Additionally, on the basis of secondary pore inversion results, another new method of formation evaluation is also proposed in the discussion part of this paper. Through detailed application result analysis, the method shows a promising capability for formation evaluation of complex carbonate reservoirs dominated by various secondary pores such as holes, caves, and cracks.