Years of waterflooding researches show that Yangdachengzi reservoir possessing the same permeability level with Fuyu reservoir, has some severely problems, such as more rapid increasing of water cut, higher water injection pressure and poorer development effect. In order to study the influence factors for these problems, micro pore structure of Yangdachengzi reservoir was investigated. Firstly, the micro pore structure of 18 natural cores in Yangdachengzi and Fuyu reservoirs with different permeability levels, including throat radius, pore radius, pore throat ratio and coordination number were compared using CT scanning and constant velocity mercury injection technology respectively, in order to find out the distribution frequency and variation rules of micro pore structure. Then, the most controlling micro pore structure parameter affecting reservoir permeability was investigated using multi parameter linear regression analysis method. Finally, the pore structure parameters were compared with those of Fuyu oil layer with the same permeability level to explain the reasons for poor physical properties and difficult development of Yangdachengzi oil layer. The results show that the average pore radius difference is less than 1% between the Yangdachengzi and Fuyu reservoir with the same reservoir permeability, while the throat radius, pore throat ratio, coordination number and other microscopic pore structure parameters exhibit significant differences of 17.4%, 8.9% and 5.2% respectively, which are the key factors determining the reservoir seepage capacity.