In order to probe the activity of the inner disk flow and its effect on the neutron star surface emissions, we carried out the timing analysis of the Rossi X-Ray Timing Explorer (RXTE) observations of the millisecond X-ray pulsar XTE J1807--294, focusing on its correlated behaviors in X-ray intensities, hardness ratios, pulse profiles and power density spectra. The source was observed to have a serial of broad puny flares on a timescale of hours to days on the top of a decaying outburst in March 2003. In the flares, the spectra are softened and the pulse profiles become more sinusoidal. The frequency of kilohertz quasi-periodic oscillation (kHz QPO) is found to be positively related to the X-ray count rate in the flares. These features observed in the flares could be due to the accreting flow inhomogeneities. It is noticed that the fractional pulse amplitude increases with the flare intensities in a range of $sim 2%-14%$, comparable to those observed in the thermonuclear bursts of the millisecond X-ray pulsar XTE J1814--338, whereas it remains at about 6.5% in the normal state. Such a significant variation of the pulse profile in the puny flares may reflect the changes of physical parameters in the inner disk accretion region. Furthermore, we noticed an overall positive correlation between the kHz QPO frequency and the fractional pulse amplitude, which could be the first evidence representing that the neutron-star surface emission properties are very sensitive to the disk flow inhomogeneities. This effect should be cautiously considered in the burst oscillation studies.
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