Signals received at the interrogator of an RFID system always suffer from various kinds of channel deformation factors, such as the path loss of the wireless channel, insufficient channel bandwidth resulted from the multipath propagation, and the carrier frequency offset between tags and interrogators. In this paper we proposed a novel Viterbi-based algorithm for joint detection of data sequence and compensation of distorted signal waveform. With the assumption that the transmission clock is exactly synchronized at the reader, the proposed algorithm takes advantage of the structured data-encoded waveform to represent the modulation scheme of the RFID system as a trellis diagram and then the Viterbi algorithm is applicable to perform data sequence estimation. Furthermore, to compensate the distorted symbol waveform, the proposed Jiggle-Viterbi algorithm generates two substates, each corresponding to a variant structure waveform with adjustable temporal support, so that the symbol waveform deformation can be compensated and therefore yield a significant better performance in terms of bit error rate. Computer simulations shows that even in the presence of a moderate carrier frequency offset, the proposed approach can work out with an acceptable accuracy on data sequence detection.