BeiDou Navigation Satellite System (BDS) receiver cannot navigation solution with less than four satellites signal in challenge environment, such as urban canyons or forests. The position accuracy in the vertical direction is frequently challenged in comparison with the one in the horizontal direction. Using chip scale atomic clock (CSAC) in the receiver can improve the positioning accuracy of the system, especially in the vertical direction. The atomic clock has high stability and can predict the clock bias with high precision. User position can be solved by only three satellites measurements and the availability of the system is improved. If more observations can still be obtained, the redundant measurements can be used to improve positioning accuracy, availability and reliability of the system. The article first analyzes of the effect of clock on the performance of the receiver. The prediction method of clock bias is determined by the analysis of the type of clock bias noise, and prediction accuracy is 3ns in 60 minutes. Then, the atomic clocks aided BDS positioning algorithm is analyzed. Finally, positioning experiment of the atomic clock aided BDS in simulation challenge environment is carried out, and the positioning result is analyzed. The results show that the accuracy of the vertical positioning in challenge environment (3 satellites) is consistent with that of the open environment in one hour, and the availability of the receiver has been greatly improved, but the precision of horizontal positioning is slightly reduced.