According to the Einstein diffusion equation，the effective diffusion coefficient of nano-fluid in biological tissues is calculated using the Monte Carlo method. The biological tissues are assumed as porous media by observing their anatomical structures. The influences of some key structural factors of porous media on the effective diffusion coefficient of nano-fluid are analyzed. The considered structural factors include shape (i.e. circle，ellipse)，size，and permutation (i.e. parallel permutation and compartmental permutation). The results indicate that the effective diffusion coefficient of nano-fluid in circular porous media are greater than that in ellipsoidal ones and it increases in proportion to the porosity of porous media. Moreover，the increase of inclusion size under the same porosity leads to the decrease of the effective diffusion coefficient. In addition，it is found that a phenomenon of “pocket effect” is existed during the transport process of nano-fluid in porous media when the sizes of pores are comparatively smaller than that of the inclusions. The particles will be trapped in this kind of “pocket shape” without getting out of it，which will drastically decrease the effective diffusion coefficient of nano-fluid. The simulation results are in good agreement with the calculated values obtained from theoretical formula，and the validity of this method is verified by the experimental data from references.