The rules are incompatible; only the setting is shared
Wizards of the Coast and AEG's Legend of the Five Rings, Second Edition uses the roll-and-keep system. Wizards of the Coast's Dungeons and Dragons, Third Edition (and, later, the 3.5 revision) uses the d20 System. While Wizards of the Coast's Oriental Adventures product uses Rokugan as its featured setting, and Legend of the Five Rings also has as its setting Rokugan, the two game systems are wholly incompatible.
Starting with Way of the Samurai (March 2002) and through The Hidden Emperor (Sept. 2005), AEG's line of officially-licensed-from-Wizards-of-the-Coast Oriental Adventures products were, however, dual-stat books—that is, the books contained information on how to use the text with both Legend of the Five Rings, Second Edition, and Dungeons and Dragons, Third Edition (the line, so far I know, never having officially embraced the 3.5 revision). The presence of statistics for both games in the same book didn't make the two game systems any more compatible, though.
In theory, the dual-stat experiment should've meant increasing the audience for the books, but, in practice, seemed to weaken both systems, content suffering as a result, although the d20 System glut likely didn't help matters. AEG tried a similar experiment with Seventh Sea and the Swashbuckling Adventures line (which wasn't offcially licensed by Wizards of the Coast) with similar lackluster results.