"lime tree," 1570s, noun use of an adjective, "of linden wood," from Old English lind "linden" (n.), from Proto-Germanic *lindjo (source also of Old Saxon linda, Old Norse lind, Old High German linta, German linde), probably from PIE *lent-o- "flexible" (see lithe); with reference to the tree's pliant bast. Compare Russian lutĭijó "forest of lime trees," Polish łęt "switch, twig," Lithuanian lenta "board, plank."
For modern tree names from adjectives, compare aspen. OED suggests the use of the adjective as a noun is at least partly creditable to "translations of a German romance" (German linden is the plural form and the form used in compounds).