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. (Using translation from Nasāʾī 1699)
أَنَّ رَسُولَ اللهِ ﷺ كَانَ يُوتِرُ بِثَلَاثِ رَكَعَاتٍ يَقْرَأُ فِي الْأُولَى بِسَبِّحِ اسْمَ رَبِّكَ الْأَعْلَى وَفِي الثَّانِيَةِ بِقُلْ يَا أَيُّهَا الْكَافِرُونَ وَفِي الثَّالِثَةِ بِقُلْ هُوَ اللهُ أَحَدٌ وَيَقْنُتُ قَبْلَ الرُّكُوعِ فإِذَا فَرَغَ قَالَ عِنْدَ فَرَاغِهِ «سُبْحَانَ الْمَلِكِ الْقُدُّوسِ» ثَلَاثَ مَرَّاتٍ يُطِيلُ فِي آخِرِهِنَّ