Samayasāra presents itself as a continuous sequence of Prakrit gāthās, traditionally counted as 415 verses, without formal chapter headings assigned by the author. The verses are composed in Jain Śaurasenī Prākrit and follow metrical patterns such as the āryā, which are characteristic of early Jain philosophical poetry. Rather than explicit chapters, the work unfolds through thematic clusters that naturally cohere around central doctrinal concerns. This gives the text a fluid yet discernible progression, moving from foundational ontological reflections toward more subtle analyses of realization and liberation.

The internal organization is best understood as a series of doctrinally ordered sections, later made more explicit by commentators who group the verses into topical units. These clusters revolve around themes such as the nature of jīva and ajīva, the distinction between the real standpoint (niścaya naya) and the practical standpoint (vyavahāra naya), the nature of bondage and liberation, and the triad of right faith, right knowledge, and right conduct. A recurring structural rhythm appears in many sequences: a doctrine is first stated from the real standpoint, then related to or contrasted with the practical standpoint, and finally clarified in favor of the pure self revealed through the real standpoint. In this way, the text repeatedly draws the reader back from worldly identifications to the standpoint of the soul as pure consciousness.

A notable feature of the verse-organization is the frequent use of negation followed by a more refined affirmation. Verses often deny that the self is identical with body, senses, mind, karmas, or actions, and then affirm the self as pure knowing consciousness. Short runs of verses will take up a single idea—such as the soul as non-doer and non-enjoyer, or the distinction between substance and modes—and work it through from several angles, giving the text a meditative, spiraling quality rather than a rigidly linear argument. Over the whole, there is a discernible movement from ontology (what the soul is), through epistemology and ethics (how it is rightly known and lived), toward the description of the realized soul and the state of liberation.

Later commentators, especially in Sanskrit expository works, have provided more explicit structural scaffolding by assigning titles and grouping verses into doctrinal sections. These commentarial arrangements do not alter the original sequence but make its implicit order more transparent, presenting a graded path from misidentification and bondage to discrimination, abidance in the pure self, and mokṣa. Thus, the organization of Samayasāra can be seen as both simple and profound: a single continuous chain of verses whose inner architecture is revealed through recurring patterns of standpoint, negation and affirmation, and progressive deepening of insight into the nature of the soul.