Beidou Satellite Navigation System (BDS) navigation receiver has the functions of Positioning, Navigation, and Timing (PNT) and message communication, and has been widely used in various industries. Under the background of the smooth transition from BDS-2 regional system to BDS-3 global system, its influence on the service performance of the navigation receiver and countermeasures are studied. The differences between BDS-2 and BDS-3 in signal type, signal system, constellation scale and service performance are compared, and the specific manifestations and state change trends of BDS smooth transition are expounded. The impact of the smooth transition of BDS on the service performance of navigation receiver is analyzed emphatically, including navigation and positioning, message communication and anti-suppression-jamming ability. The simulation results show that the RDSS message communication service can still be used normally during the smooth transition period of BDS-2 receiver ( PRN01～37). With the progressive retirement of BDS-2 satellite, the number of satellites available in space will gradually decrease from 33 to 18, the average number of satellites visible worldwide will decrease from 11.62 to 6.31, the average Geometric Dilution Precision (GDOP) value will increase from 2.00 to 3.15, and the continuous availability of services will decrease from 93% to 46.46%, which will affect the positioning accuracy and service range. When the power of BDS-3 satellite is enhanced, the navigation receiver can obtain 7～15 dB improvement in anti-suppression-jamming ability. According to the different application scenarios of the navigation receiver, the corresponding countermeasures are given to weaken or eliminate the impact, so that the navigation receiver can continuously provide reliable services for users during the smooth transition of the BDS. The research results can provide reference for the design, development and application of BDS navigation receivers.