Natural fractures are widely distributed in rocks. Generally, there are four types of natural fractures, i.e., single, parallel, intersected and mixed. Uniaxial compression tests on naturally fractured marble samples, taken from the transportation tunnels of Jinpin II hydropower station in southwestern China, are conducted with a MTS815 rock mechanics testing system. The acoustic emission (AE) events are monitored by PCI-II AE system. The spatial evolutions of different natural fractures have been successfully located and tracked according to the AE ringing number. Experimental results indicate that the failure process of fractured marble is locally progressive. The AE event accumulation is strongly related to the loading process and stress redistribution in rock. For the former two types, i.e., single and parallel natural fractures, the spatial AE event distributions in marbles are relatively simpler than those of the other two. The corresponding strong AE event numbers (with ringing number greater than 20) increase with the compressive stress along the naturally fractured surfaces when the stress is low. When the compressive stress is close to the failure strength of the rock, AE events first appear around the natural fracture tip, then spread along the final rupture direction. For the marble containing intersected natural fractures, strong AE events are approximately uniformly distributed at the initial stage of the compression test. Later, the AE events increase when the compressive stress gets higher continuously, and then concentrate around the intersection points of fractures. The case with mixed natural fractures has the most complex AE event distribution than those of the others. However, it is still not difficult to determine the internal weakness parts and stress field based on the spatial AE event distribution. The fractal dimension of the spatial AE event distribution, capable of describing the mechanical behavior and structural damage of rock materials, is estimated by a newly developed analysis method. The parameters of AE events for different types of natural fractures, such as AE accumulative value, amplitude and absolute energy, are statistically analyzed. The present testing scheme can be an initial step toward further development of in situ microseismic monitoring techniques for complex fractures. Moreover, the obtained experimental and analytical results can facilitate the investigation on rock mass failure and instability mechanism.