  This study reports pulse variation analysis results for the forth discovered
accretion-powered millisecond pulsar XTE J1807-294 during its 2003 outburst
observed by {\it Rossi X-ray Timing Explorer}. The pulsation is significantly
detected only in the first $\sim$90d out of $\sim$150d observations. The pulse
phase variation is too complex to be described as an orbital motion plus a
simple polynomial model. The precise orbital parameters with
$P_{orb}=40.073601(8)$ min and ${\it a_x}\sin {\it i}=4.823(5)$ lt-ms were
obtained after applying the trend removal to the daily observed 150s segments
pulse phases folded with a constant spin frequency without Keplerian orbit
included. The binary barycenter corrected pulse phases show smooth evolution
and clear negative phase shifts coincident with the flares seen on the light
curve and the enhancements of fractional pulse amplitude. The non-flare pulse
phases for the first $\sim$60d data are well described as a fourth order
polynomial implying that the neutron star was spun-up during the first
$\sim$60d with a rate $\dot \nu=(1.7\pm0.3) \times 10^{-13}$ Hz/s at the
beginning of the outburst. Significant soft phase lags up to $\sim$500 $\mu s$
($\sim$10% cycle) between 2 to 20 keV were detected for the nonflare pulse
phases. We conclude that the anomalous phase shifts are unlikely due to the
accretion torque but could result from the ``hot spot'' moving on the surface
of neutron star.
