This article compares ethnomethodology to social systems theory and attempts to clarify their theoretical concerns, differences and similarities when synthetically considering the former as a practical logic of the latter. As two poles on a continuum of research methods, ethnomethodology is a microanalysis of social order and human agency, whereas systems theory assumes a macro and theoretical abstraction of system formation and social evolution. When attempts are made to solve the problems of the micro/macro, part/whole, or individual/society relation, this comparison is conducive to elucidating how the practical logic is implied on both micro and macro sides, and to enhance our understanding of the human social world. Three points are suggested. First, systems theory and ethnomethodology do not contradict each other; they are complementary in an intricately dialectical process. Second, ethnomethodology can be observed through indexical rather than objective expressions. Third, due to a higher level of abstraction of systems theory, this article argues that ethnomethodology can possibly be utilized to explicate and also be regarded as the practical logic of systems theory. This comparison may contribute to reformulating systems theory, and also to some philosophical puzzles.