Evolution of languages has always been of interest to linguists. In this paper we study the natural progress of the syllable structure from Old Persian (O.P) to Middle Persian (Mi.P) and up to the Modern Persian (Mo.P). For this purpose all the words containing consonant sequences are collected from specific sources of each of these languages, and then analysed according to the syllabification principles. Pulgram (1970) distinguishes three principles for this matter which is stated in Hyman (2003:279).The first one, is the maximum open syllable principle, the second, the minimum coda and maximum onset principle and the last one is the irregular coda principle. In addition , to find the syllable structure of the words, phonological rules are also applied. Greenberg (1978) suggests a number of rules specifying the collocation constraint of phonemes and phonological structure of the word, which are: Obligatory Contour Principle (OCP), Sonority Sequencing Principle (SSP) and Syllable Contact Law (SCL). On basis of these rules and principles the clusters are separated from sequences, and the syllable structure of each language is acquired. Finally the progress of the syllable structure change is studied through representing the data from all three languages, and investigating the process taken for clusters to reach the present time. As the data exhibits, in O.P initial consonant clusters are frequently observed and also, through syllabification, some final syllable clusters will be obtained. In Mi.P also both initial and final clusters fully exist, with growing number of final ones. Initial consonant clusters are completely omitted in Mo.P and only final clusters remain. Deletion and vowel insertion are the two most occurring processes in these processes.