In the natural system, physical, chemical, and biological weathering processes play important roles in the formation of fine particles including nanoparticles. However, information on the nature, physicochemical properties and environmental fate of nanoparticles is severely lacking. Traditionally, nanoparticles were neglected in environmental research, because particles smaller than 450 nm are classified as soluble by convention. An innovative device developed in the present study for high efficiency collection of nanoparticles provides a sound basis for the separation of nanoparticles. Zeolite A was used to demonstrate its structural transformation from well crystalline to short-range-ordered (SRO) particles including nanoparticle in the range of 450-2000, 100-450, 25-100 and 1-25 nm. With decreasing the particle size, the T (Si, Al)-O asymmetric and symmetric stretching vibrations shifted toward higher IR frequencies and the Si to Al molar ratio increased consistently from 1.8 to 5.2, which is attributed to the loss of the external linkage D-4R units of the structure. The data obtained in this study show, for the first time, unequivocal evidence of physicochemical weathering-induced structural alteration of zeolite in various size fractions from well crystalline colloids to poorly crystalline to non-crystalline nanoparticles and finally to sodalite structure. This is accompanied by the enhancement of the specific surface area of the 1-25 nm fractions by more than one order of magnitude compared with the bulk sample (<2000 nm). Knowledge on the transformation of zeolite into its nanoparticles, which is, in turn, related to the kinetics and mechanisms of mineral weathering through physicochemical reactions, is of fundamental significance in understanding the development of nanoparticles in natural environments and the impact on ecosystem integrity.