Vapor cell rubidium atomic clock is widely used in the fields of satellite navigation and communication with advantages including small size, light weight, low power and maintenance cost. The high-performance vapor cell rubidium atomic clocks in BDS-3 (Beidou-3 Navigation Satellite System) demonstrate exceptional stability, achieving 5E-13/ τ−−√ within 1~10 000 s and exceeding 3E-15 at one day. However, in atmospheric environment, due to environmental factors, particularly the influence of atmospheric pressure, the long-term stability deteriorates by 1 to 2 orders of magnitude after 1 000 s. This paper proposes a high-precision pressure compensation method by analyzing noise introduced from compensation algorithm and conducting sufficient experimental verification. After compensation, the long-term stability at 10 000 s of ground-type rubidium atomic clock is improved by approximately one order of magnitude, reaching a frequency stability better than 6.5E-15.