By dividing the evolution of the U.S. clinical trial registration system into three phases—emergence, inception, and maturity—this study systematically traces its half-century development and reveals the underlying tensions and institutional logic. The U.S. clinical trial registration system is not merely a technical instrument, but a comprehensive institutional platform reconciling the conflicts among scientific rationality, commercial interests, and the public’s right to know. The emergence phase (1971—1985) originated from the establishment and public disclosure of the International Cancer Database to meet cancer research needs and safeguard patients’ survival rights. The inception phase (1986—2004) unfolded against the backdrop of the FDA’s drug approval crisis, with the construction of major disease registration systems breaking the regulatory deadlock and achieving an “incremental revolution”. The maturity phase (2004—2016) centered on controlling publication bias and advancing institutionalization and legalization. The 2004 paroxetine incident galvanized global consensus on trial registration, and the 2007 U.S. Congressional mandate marked the pivotal turning point toward a fully mature system. Today, China still faces low registration rates and insufficient legal constraints. Drawing on the U.S. experience, China should prioritize institutional publicness, legal enforceability, and the containment of publication bias to strategically upgrade its clinical trial registration system.