Abd al-Aziz bin Jurayj (may Allah have mercy on him) said: We asked Sayyidah Aishah (may Allah be pleased with her) what the Prophet (peace and blessings be upon him) used to recite in witr. She said: In the first rak'ah he (peace and blessings be upon him) would recite "Glorify the name of your Lord, the Most High" [Surah al-A'la: 1], in the second rak'ah "Say: O disbelievers" [Surah al-Kafirun: 1], and in the third rak'ah "Say: He is Allah, the One" [Surah al-Ikhlas: 1] and the Mu'awwidhatayn (the two surahs of seeking refuge).
Hadith Referenceالسنن الكبرى للبيهقي / كتاب الصلاة / 4854