Oceanic crust at fast-spreading ridges is formed by melt percolating through the Mohorovičić Transition Zone (MTZ), the boundary between crust and mantle. However, the relationship between the crustal structures and MTZ remains elusive. Applying full waveform inversion to wide-angle seismic data acquired near the 9oN East Pacific Rise, we show that the variations in crustal MTZ thicknesses are inversely correlated along the segment, although their total cumulative thickness shows little variations. These variations could be attributed to different melt migration efficiency through MTZ or variation in mantle thermal structures. Thin MTZ could be due to rapid percolation of melt from mantle to crust whereas the thick MTZ results from the crystallization of melt within the transition zone. On the other hand, for relatively hot segments, melt will accumulate at shallower depth within the lower crust. In contrast, melt could freeze at Moho depth for relatively cold segments thickening the MTZ.