“Lü, diao, pu, qi” (temperament, mode, notation, and instruments) form the core conceptual framework of traditional Chinese music theory and serve as fundamental theoretical dimensions for understanding the intrinsic characteristics of traditional music. Influenced by the culture-oriented and practice-focused approaches of ethnomusicology, this study integrates the contents of theoretical research with the pedagogical and performative practices of folk musicians. Focusing on Fujian Nanyin, which is a tradition that continues to widely employ gongche notation in its transmission, the article explores how its rich theoretical system is documented and transmitted through different notational logics embedded in gongche notation, and how these in turn shape its performance practice. The study proposes that the theoretical content of Nanyin is constituted by two behavioral layers and components: first, the normative elements formed through notation and transmission, which are not to be altered arbitrarily; and second, the creative variables that emerge in performance. It argues that the behavioral patterns in musicians' practice also provide an important pathway for recognizing and analyzing the characteristics of Nanyin's theoretical system.