We report on changes of the cyclotron resonance energies of the recurrent transient pulsar, X0331+53 (V0332+53). The whole RXTE data acquired in the 2004-2005 outburst were utilized. The 3-80 keV source luminosity varied between 1.7x10^36 and 3.5x10^38 ers/s, assuming a distance of 7 kpc. We confirmed that the fundamental cyclotron resonance energy changed from ~22 to ~27 keV in a clear anti-correlation to the source luminosity, and without any hysteresis effects between the rising and declining phases of the outburst. In contrast, the second harmonic energy changed from ~49 to ~54 keV, implying a weaker fractional change as a function of the luminosity. As a result, the observed resonance energy ratio between the second harmonic and the fundamental was ~2.2 when the source was most luminous, whereas the ratio decreased to the nominal value of 2.0 at the least luminous state. Although the significance of this effect is model dependent, these results suggest that the fundamental and second harmonic resonances represent different heights in the accretion column, depending on the mass accretion rate.