Mid-ocean ridge basalts (MORBs) from East Pacific Rise (EPR) 13°N are analysed for major and trace elements, both of which show a continuous evolving trend. Positive MgO–Al2O3 and negative MgO–Sc relationships manifest the cotectic crystallization of plagioclase and olivine, which exist with the presence of plagioclase and olivine phenocrysts and the absence of clinopyroxene phenocrysts. However, the fractionation of clinopyroxene is proven by the positive correlation of MgO and CaO. Thus, MORB samples are believed to show a “clinopyroxene paradox”. The highest magnesium-bearing MORB sample E13-3B (MgO=9.52%) is modelled for isobaric crystallization with COMAGMAT at different pressures. Observed CaO/Al2O3 ratios can be derived from E13-3B only by fractional crystallization at pressure >4 ±1 kbar, which necessitates clinopyroxene crystallization and is not consistent with cotectic crystallization of olivine plus plagioclase in the magma chamber (at pressure ~1 kbar). The initial compositions of the melt inclusions, which could represent potential parental magmas, are reconstructed by correcting for post-entrapment crystallization (PEC). The simulated crystallization of initial melt inclusions also produce observed CaO/Al2O3 ratios only at >4±1 kbar, in which clinopyroxene takes part in crystallization. It is suggested that MORB magmas have experienced clinopyroxene fractionation in the lower crust, in and below the Moho transition zone. The MORB magmas have experienced transition from clinopyroxene+plagioclase+olivine crystallization at >4±1 kbar to mainly olivine+plagioclase crystallization at <1 kbar, which contributes to the explanation of the “clinopyroxene paradox”.