Under the atmospheric multipath conditions, both canonical transform (CT) and full spectrum inversion (FSI) method can solve the problem of calculating bending angle profiles within the multipath area. The atmospheric propagation of GPS signals under atmospheric multipath conditions is simulated using multiple phase screens (MPS) technique. Bending angle profiles computed by CT method are compared with corresponding solutions to Abel integral (taken as the true value). The results show that CT method is close to the true value in the multipath area. The retrieval accuracy of CT method is degraded to some extent when Gaussian noises are added to the phase of simulated signal. About 4500 COSMIC (Constellation Observing System for Meteorology, Ionosphere and Climate) atmPhs profiles from DOY (day of year) 71 to DOY 73 in 2007 are retrieved by CT method. Statistical comparisons of the retrieved refractivity profiles, together with atmPrf data (retrieved by FSI method), with those from corresponding ECMWF (European Centre for Medium-Range Weather Forecasts) analysis show that CT method contains greater systematic negative bias than atmPrf data below 5 km. A possible reason is that the signal aperture is decreased for back-propagating the signal from LEO position to the back-propagation plane in CT method. The small aperture means low accuracy in the refractivity. The influence of signal truncation on both retrieval accuracy and occultation number is also discussed.