In the moist lower troposphere, traditional phase-locked loop tracking of GPS (Global Position System) signal will introduce errors in the retrieved results. Both internal and external method can be used to remove navigation data modulation (NDM) and accurately recover the phase of GPS signals recorded in open-loop mode. The internal method removes the NDM using relationship between adjacent samples, while the external method removes the NDM using the externally recorded NDM bit data. Both above-mentioned methods are used to process the constellation observing system for meteorology, ionosphere and climate (COSMIC) radio occultation data. COSMIC case study shows that internal method may include half-cycle slip in the recovered phase, which will lead to error in the retrieved refractivity. About 3130 COSMIC radio occultation soundings recorded in open-loop mode are processed by the internal and external method, and statistical comparison results of retrieved refractivity with that from the European Centre for medium-range weather forecasts (ECMWF) analyses show that the external method has a better penetration ability than the internal method in the lower moist troposphere. The mean of fractional difference in refractivity retrieved by external method is smaller than that by internal method below about 3 km.