Aiming at the range ambiguity problem of radar for near space hypersonic target, the existing track before detect (TBD) algorithm cannot detect the target effectively through the long time accumulation, a kind of Hough transform (HT) TBD (HT-TBD) algorithm based on multiple frequency and multiple hypotheses is proposed. Firstly, several pulse repetition frequencies (PRF) are worked alternately to detect the target and get the initial measurement data. At this time, the distance measurement of the initial measurement is ambiguous. Then, the multiple hypotheses extending is made on all the possible ambiguous intervals to get the multiple hypotheses extending measurement data. Finally, the extended measurement data are used for time-radial distance plane HT. The target track could be obtained after HT-TBD algorithm, and the range ambiguity could be resolved at the same time. The validity of the algorithm is verified by simulation, and the algorithm performance under different SNR and clutter density is detailedly analyzed. The simulation results show that the near space hypersonic target under the condition of range ambiguity can be effectively detected according to the algorithm in this paper.