Yongle atoll in the Xisha (Paracel) Archipelago is an isolated carbonate platform developed on Precambrian metamorphic and Mesozoic volcanic rocks since the early Miocene. To identify the 3D stratigraphic architecture and evolution of this platform, 13 high-resolution seismic profiles and shallow-to-deep water multi-beam data were processed and analyzed to reveal seismic facies, sequence boundary reflectors, seismic units, and platform architecture. Nine types of seismic facies were recognized based on their geometry, which included seismic amplitude, continuity, and termination patterns; additionally, six reflections, i.e., Tg, T60, T50, T40, T30, and T20, were identified in the Cenozoic strata. Five seismic units, SQ1 (lower Miocene), SQ2 (middle Miocene), SQ3 (upper Miocene), SQ4 (Pliocene), and SQ5 (Quaternary), were identified from bottom to top across the platform. The platform grew rapidly in the middle Miocene and backstepped in the late Miocene–Pliocene. Here, we discuss the developmental characteristics and evolution of the Yongle Atoll, in combination with drilling wells, which can be divided into four stages: the initiation stage in the early Miocene, the flourishing stage in the middle Miocene, the partial-drowning stage in the late Miocene–Pliocene, and modern atoll in the Quaternary.