The rapid accumulation of empirical data spanning environmental stress, secondary metabolism, ethnopharmacology, and bioactive therapeutics has generated a vast yet fragmented corpus of literature. Existing reviews often concentrate on narrow empirical outcomes or isolated bioactivities, neglecting the overarching methodological and epistemological architecture governing the field. This study systematically analyzes and classifies 39 foundational studies and syntheses across six primary thematic clusters—ranging from global biome dynamics and ethnopharmacology to metabolic bioengineering and abiotic stress adaptations—using Cooper’s (1988) taxonomy across its six foundational dimensions: focus, goal, perspective, coverage, organization, and audience. Our analysis reveals that the prevailing focus centers disproportionately on research outcomes (such as secondary metabolite yield, radical scavenging capacities, and physiological stress responses), leaving underlying biochemical theories and regulatory practices comparatively underrepresented. In terms of goal, synthesis and integration predominate over the critical appraisal of experimental methodologies or identification of central policy bottlenecks. A neutral perspective characterizes the vast majority of thematic syntheses and empirical trials, while explicit espousal or directive positions remain confined to health policy, regulatory compliance, and macromolecular drug delivery. Coverage is predominantly purposive or representative across multi-species syntheses, contrasting with single-case empirical factorial designs. Structurally, thematic and conceptual arrangements supersede chronological frameworks, reflecting a topic-driven research paradigm. Finally, the target audience remains heavily stratified toward specialized scholars in plant physiology and pharmacology, highlighting an urgent need for translation toward policymakers, agro-industrial practitioners, and clinical researchers. These findings elucidate current trajectories in plant secondary metabolism research and establish an objective structural baseline for future meta-syntheses and cross-disciplinary translations.