The Ordovician carbonate reservoirs in the Tarim Basin with secondary dissolution pores and vugs have complicated pore structures. The weathering crust reservoirs mainly consist of large cavities or vugs connected by fractures, but most of the reef-shoal reservoirs have complex and small throats among matrix pores. The pore structure can be divided into four types: big pore and big throat, big pore but small throat, small pore and small throat, and fracture type. Most of the average throat radius falls between 0.03 and 0.07 μm, close to that of unconventional reservoirs except in local areas with developed fractures. Fluid driving force analysis shows that the differentiation of fluid is mainly controlled by the throat radius in two kinds of mechanism separated by the critical throat radius about 0.1 μm. There is obvious fluid differentiation and oil/gas/water contact in fracture-cavity reservoirs with big throats. However, most of reservoirs under the critical throat radius have high capillary pressure, which resulted in incomplete differentiation of gas/oil/water, and complicated fluid distribution and fluid properties in the unconventional reservoirs.