In this paper, the authors employ three different types of dye molecules, Nile red, Rhodamine 6G, fluorescein and a fluorescent protein-R-phycoerythrin (R-PE).The Rhodamine 6G is positively charged molecules, fluorescein is negatively charged molecules, and Nile red is neutral molecules.The R-phycoerythrins have either a net positive or negative charge which is balanced at the isoelectric point (4.22).It is negatively charged molecules also under our experimental condition.The Nile red, rhodamine 6G, fluorescein and R-phycoerythrin are trapped into alginate calcium hollow capsule respectively.The diffusion processes of those molecules from calcium alginate capsule to solution are measured based on a fluorescence method.The results indicate that electrical characteristics of encapsulated molecules have effect on their diffusion behaviors.The positively charged rhodamine 6G is well accordance with a model of control release from porous polymer membranes.The neutral molecules not only can be released from porous polymer framework, they also can directly dissolve out through polymer membrane.The electrostatic repulsion between fluorescein and negatively charged calcium alginate membranes will accelerate the molecular motion, which is propitious to molecules directly dissolving out through polymer membrane.Based on Fick’s law of diffusion, R-PEs can be releases from porous polymer framework.It shows the longest equilibrium time.Comparing neutral molecules, negatively and positively charge molecules show the stronger interaction on electric polymer membrane, which results in that the diffusion coefficients of rhodamine 6G and fluorescein are less than that of neutral molecule Nile red.The consequences obtained here should readily explain analogous control releasing behaviors of other functional molecules.