Due to its unique biogenesis, forming environment and deposition process, calcareous sand is featured with irregularity, brittleness, weak structure and low cohesion, and is considered substantially different from the common terrestrial sand deposits. Fine particles bonded with weak cohesion may be resolved by osmotic action and then migrate and reaccumulate, thus causing changes in porosity and permeability. This study has carried out filtration experiment and laser particle size analysis of exudate sediment under different initial conditions to analyze the principles of evolution, involving permeability coefficient and the characteristics of fine particle transporting during the filtration process in calcareous sand. The results show that the loss of fine particles tends to occur under the seepage condition, and that results in the local changes of soil structure and permeability. The factors including the grading, compactness and percolation hydraulic gradient play important roles in fine grain loss in the process of filtration. The results show that the higher soil coarse grain content is, the lower degree of compactness is, and the larger percolation hydraulic gradient is, which lead to the loss of fine particles easily and additionally, enlarging the size of losing particles as well as range of permeability variation. The main particle size range of fine grain loss during calcareous sand filtration is significantly affected by grading. The smaller the content of coarse grain in grading results in smaller particle size of grain loss, and vice versa.