This study investigates the emergence, operation, and structural transformation of specialized trial organizations (STOs) in China, focusing on those established in the fields of intellectual property (IP) and environmental law. Although both legal domains experienced the widespread establishment of specialized tribunals, only IP law led to the development of specialized courts. This raises an empirical puzzle: Why did STOs in these two fields diverge in their structural trajectories despite undergoing similar patterns of initial institutional expansion? What explains the differing paths of structural change in the development of STOs across IP and environmental law? Employing a processual approach, this study conceptualizes STOs as knowledge-making sites whose operations are shaped by how legal knowledge is generated through lawmaking and subsequently applied in judicial practice. Drawing on over 160 units of ethnographic data collected during five years of fieldwork—alongside in-depth textual analysis of news articles, judicial interpretations, and government documents—this research reveals how differences in the relationship between the generation and application of legal knowledge gave rise to distinct operational modes within STOs: progressive, robust, and conservative. These modes, shaped by the institutional boundaries within which STOs are embedded and by the judicial epistemologies produced through interactions between judges and trial participants, influenced how static court operations were encoded and carried forward over time. In IP law, an early convergence around the progressive mode facilitated the coherent encoding of judicial experience, ultimately supporting the establishment of specialized IP courts. In contrast, environmental tribunals exhibited operational fragmentation and region-specific encoding trajectories, which hindered institutional learning and failed to justify structural expansion. This comparative analysis underscores the central role of courts’ dynamic operation—or the “encoded historicality of court operation”—in shaping long-term institutional development, offering new insights into judicial politics, the organizational logic of judicial reform, and the study of legal change.