Study on the effectiveness of fractures is of great significance for understanding reservoir types and properties, identifying reservoir seepage mechanisms and delineating the reasonable development technologies and policies. In this paper, the Changxing reef-flat facies reservoirs in the Yuanba area, Sichuan Basin, was taken as an example. After the characteristics of natural fractures were evaluated, the effectiveness of different types of fractures was investigated by using core, thin section, imaging logging and production performance data. Then, the main geological factors that influence fracture effectiveness were analyzed, and the development significance of effective fractures was illustrated. The following results are obtained. (1) Structural fractures and diagenetic fractures are mainly developed in Changxing Fm carbonate reservoirs in Yuanba area. Structural fractures include shear fractures and extensional fractures, and diagenetic fractures include dissolution fractures, structural-dissolution fractures and pressure-solution fractures. (2) High-angle structural fractures are the most effective, followed by horizontal fractures and then oblique fractures, and pressure-solution fractures are the least effective. (3) Among structural fractures, those of NW–SE and nearly E–W oriented are more effective than those of the NE–SW oriented. (4) The earlier the fractures are formed, the more likely they are to be filled with calcite or dolomite and become invalid. (5) The fractures which are formed before or during the oil and gas charging tend to be filled with organic matters and become invalid. The late fractures which are formed after oil and gas charging are mostly effective and their contribution to the reservoir is the greatest. (6) The fractures nearly parallel to the maximum principal stress direction of current ground stress present good effectiveness with large opening. It is concluded that the opening and filling features of natural fractures help determine if fractures are effective or not, and the development degree, distribution and combination features of effective fractures and the matching relationship between fractures and pores further dominate the development significance of effective fractures; that when the effective fractures are more developed and are connected with each other to form a large-scale fracture network, separated and isolated pores and dissolved fractures and cavities can be connected, as a result, the physical properties of reservoirs are improved and high production rates of gas wells are realized.