What to Recite in the Three Rakats of Witr Prayer
Islamic scholars state that specific Surahs are Sunnah to recite in each rakat of Witr prayer based on an authentic hadith.
The Islamic ruling about what to recite in Witr prayer is based on a narration from Aisha may Allah be pleased with her. She said that the Prophet Muhammad peace be upon him recited Surah Al Ala in the first rakat of Witr, Surah Al Kafirun in the second rakat, and in the third rakat he recited Surah Al Ikhlas, Surah Al Falaq, and Surah An Nas. This hadith is recorded in Tirmidhi 463.
Based on this hadith, Islamic scholars explained in their fatwa that if a person prays only one rakat of Witr, then after Surah Al Fatiha he should recite Surah Al Ikhlas, Surah Al Falaq, and Surah An Nas in that single rakat.
If a person prays three rakats of Witr, then it is Sunnah to recite Surah Al Ala in the first rakat, Surah Al Kafirun in the second rakat, and Surah Al Ikhlas, Surah Al Falaq, and Surah An Nas in the third rakat. This ruling is mentioned by Islamic scholars in the book Nihayat al Zayn.