In this work, a micro-model of the catalyst layer of polymer electrolyte membrane fuel cell (PEMFC) was developed. The micro-model includes the transport phenomena and the reaction kinetics within a three dimensional micro-structure representing a sample of PEMFC catalyst layer. Proper physical boundary conditions have been described on the surfaces of the sample as well as on the interfaces between the regions through which all constituents are solved in a coupled manner. A four-phase micro-structure of CL was reconstructed, the platinum particles were resolved in the computational grid generation and the governing equations were solved within platinum region. A body-fitted computational mesh was generated for the reconstructed micro-structure of CL. The number of computational cells were optimized based on how close to an analytical sphere the magnitude of the surface area of a sphere can be captured after generating the computational cells. The interfaces with important physical phenomena were more refined than the rest of the interfaces, specially the electrochemically active reaction surface. The computational mesh was checked for a grid independent numerical solution. The Knudsen effects was included by calculating the characteristic length in the pore region. Four different cases of including Knudsen effects were studied. Also, a comparison was made between solution with and without Knudsen effects. A physical model of oxygen dissolution was developed, the oxygen dissolution at the interface between pore and ionomer was treated as an superficial phenomenon. The performance curves were produced and provided for the reconstructed micro-structure along with the distribution of field variables. A length study of the reconstructed micro-structure was conducted such that the results from the micro-modeling can capture the trend in variable distributions observed in the macro-modeling of CL or experiments. A platinum loading study was preformed and the anomalous phenomena of dramatic increase in oxygen transport resistance observed in some experimental works was explained by isolating the ionomer region of the CL micro-structure and numerically calculating the shape factor for diffusive transport. It was found that the increase in oxygen transport resistance is due to the increase in diffusion pathway and decrease in the transport surface area.