The invention discloses a signal processing method and system for resistivity measurement of electromagnetic waves while drilling. The signal processing method comprises the steps that a transmitting signal with preset frequency is transmitted to a formation to be measured; a first electromagnetic wave signal and a second electromagnetic wave signal reflected back from the formation to be measured are obtained; the two electromagnetic wave signals are amplified to obtain a first amplified signal and a second amplified signal; the high and low frequency components in the two amplified signals are separated by utilizing a digital switch module, and the digital switch module is controlled by a digital switch control signal; the frequency components in the two amplified signals are filtered out; the phase difference and amplitude ratio of the low frequency components of the two amplified signals are calculated; according to the phase difference and the amplitude ratio, the resistivity of the formation to be measured is obtained. The calculation amounts required by the digital switch control module and a filter module adopted by the signal processing method and the signal processing system are small, so that the system is low in power consumption, circuits are simple, and the reliability is high.