A joint estimation and compensation method of RF imperfections in a LIE (Long Term Evolution) uplink system comprises steps: establishing a joint signal model with RF imperfections; according to the joint signal model, undertaking estimation and compensation of CFO, DC offset, multipath channel, IQ imbalance and shaping filter imbalance of a received signal; and using a frequency equalizer to equalize said received signal and determine modulation data. For reducing computational complexity, the present invention further converts the received signal from a time domain to a frequency domain to undertake frequency domain compensation. The present invention can indeed solve the problems of IQ imbalance, filter imbalance, DC offset, multipath channel and CFO and effectively estimate and compensate RF imperfections in the LTE uplink system.