The current study explains the morphophonemic variation in Saraiki language. The complete phenomenon is described through the analysis of Saraiki phonology and morphology. The data has been collected from the daily speech of Saraiki speakers and from the comparative dictionary of Indo-Aryan languages and is analysed through morpheme-based theory. The study explains how irregularity occurs in the formation of Saraiki words and exposes its morphophonemic structure as well. The study describes how this morphophonemic process works differently with different type of roots. The behaviour of same suffix varies with the variation of a root. The structure of suffix changes in different conditions when root is coda less, having coda, roots ending with /s/ and having /ɦ/ coda. The current study also elaborates the process of changing noun into verb and vice versa.