We present the results of X-ray observations of the well-studied TeV blazar Mrk 421 with the Suzaku satellite in 2006 April 28. During the observation, Mrk 421 was undergoing a large flare and the X-ray flux was variable, decreasing by ~ 50 %, from 7.8x10^{-10} to 3.7x10^{-10} erg/s/cm^2 in about 6 hours, followed by an increase by ~ 35 %. Thanks to the broad bandpass coupled with high-sensitivity of Suzaku, we measured the evolution of the spectrum over the 0.4--60 keV band in data segments as short as ~1 ksec. The data show deviations from a simple power law model, but also a clear spectral variability. The time-resolved spectra are fitted by a synchrotron model, where the observed spectrum is due to a exponentially cutoff power law distribution of electrons radiating in uniform magnetic field; this model is preferred over a broken power law. As another scenario, we separate the spectrum into steady and variable components by subtracting the spectrum in the lowest-flux period from those of other data segments. In this context, the difference (variable) spectra are all well described by a broken power law model with photon index Gamma ~ 1.6, breaking at energy epsilon_{brk} ~ 3 keV to another photon index Gamma ~ 2.1 above the break energy, differing from each other only by normalization, while the spectrum of the steady component is best described by the synchrotron model. We suggest the rapidly variable component is due to relatively localized shock (Fermi I) acceleration, while the slowly variable (steady) component is due to the superposition of shocks located at larger distance along the jet, or due to other acceleration process, such as the stochastic acceleration on magnetic turbulence (Fermi II) in the more extended region.
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