The Messenger of Allah ﷺ used to pray witr with three rak'ahs. In the first he would recite: "Glorify the Name of Your Lord, the Most High" in the second: "Say: O you disbelievers!", and in the third: "Say: He is Allah, (the) One". And he would say the Qunut before bowing, and when he finished he would say: Subhanal-Malikil-Quddus (Glory be to the Sovereign, the Most Holy) three times, elongating the words the last time.
أَنَّ رَسُولَ اللَّهِ ﷺ كَانَ يُوتِرُ بِثَلاَثِ رَكَعَاتٍ كَانَ يَقْرَأُ فِي الأُولَى بِ { سَبِّحِ اسْمَ رَبِّكَ الأَعْلَى } وَفِي الثَّانِيَةِ بِ { قُلْ يَا أَيُّهَا الْكَافِرُونَ } وَفِي الثَّالِثَةِ بِ { قُلْ هُوَ اللَّهُ أَحَدٌ } وَيَقْنُتُ قَبْلَ الرُّكُوعِ فَإِذَا فَرَغَ قَالَ عِنْدَ فَرَاغِهِ سُبْحَانَ الْمَلِكِ الْقُدُّوسِ ثَلاَثَ مَرَّاتٍ يُطِيلُ فِي آخِرِهِنَّ