Eleven conodont zones are established for the Lower Triassic of the Motianling section in the Nanpanjiang Basin, South China. Detailed size measurements on 2244 P1 conodont elements demonstrate dynamic size variation patterns during the Early Triassic that are calibrated to the Early Triassic timescale and conodont zonation. Correlation of conodont size variation with various environmental indicators show that these size changes are primarily controlled by rapidly changing and episodic environmental conditions and ecological recovery in the aftermath of the end-Permian mass extinction. Decreasing size trends occur in the early Griesbachian, late Griesbachian and at the Smithian-Spathian boundary. Episodes of size increase (rebounds) occur in the middle Griesbachian, Induan-Olenekian boundary and middle-late Spathian. The observed temporal size variations indicate that conodont animals were significantly affected by rapidly changing environmental conditions (temperature and redox conditions mainly) during the Early Triassic and recurrent size increases (rebounds) occurred during periods of environmental and climatic amelioration (climatic cooling and oxygenation) demonstrating a complicated recovery history of marine ecosystems in the aftermath of the largest Phanerozoic biotic crisis.