This study reports pulse variation analysis results for the forth discovered accretion-powered millisecond pulsar XTE Jl 807-294 during its 2003 outburst observed by Rossi Timing Explorer (RXTE). The fine orbital parameters with Porb =40.073601(8) min and ax; sin i = 4.823(5) It-ms were first obtained after applying trend removal for the daily phase drift. The binary barycenter corrected pulse phases show smooth variation plus clear negative phase shifts coincident with the flares seen on the light curve as well as enhancements of fractional pulse amplitude. The non-flare pulse phases are well described as a fourth order polynomial implying that the neutron star was spun-up during the ourburst. Significant soft phase lags up to ∼500/μs between 2 to 20 keV were detected for the non-flare pulse phases. The variations of pulse phases during the flares and their energy-dependent shifts indicate that the anomalous phase shifts are a result from the "hot spot" shifting on the surface of neutron star.