RXTE observations of the X-ray transient pulsar 2S 1417-62 between 1999 November and 2000 August with a total exposure of $sim 394$ ksec were analyzed. Observations include a main outburst followed by a series of mini outbursts. Changes in pulse morphology and pulse fraction were found to be related to the changes in X-ray flux. Particularly low X-ray flux regions were found to have significantly lower pulse fractions with different pulse morphologies. The 3-60 keV PCA-HEXTE main outburst spectrum was modeled with an absorbed power law model with high energy cut-off and a Gaussian Iron line complex feature. Using the same spectral model, individual 3-20 keV PCA spectra were found to be softer and less absorbed in low X-ray flux regions between outbursts. Spectral studies showed that hydrogen column density was correlated, and the power law index was anti-correlated with the 3-20 keV X-ray flux. X-ray flux related spectral and timing features in 2S 1417-62 except for low X-ray flux regions were interpreted as a sign of disc accretion with a similar accretion geometry with a varying mass accretion rate ($dot{M}$), whereas spectral and timing features of the low X-ray flux regions were interpreted as a sign of possible temporary accretion geometry change prior to the next periastron where $dot{M}$ increases again to restore the original accretion geometry.
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