The metropolitan resources comprehensive efficiencies (also called comprehensive technical efficiency, short for CTE, thereafter), change trends and causes are investigated using DEA and Malmquist index models, respectively, in China during the period 1990-2006. Firstly, the DEA model results show that the metropolitan CTE was just fair to middling with the characteristics of almost declining from the Eastern Coastal to Western China, and only few metropolises were DEA efficient. Secondly, the results also show that the PTE was correlated with the urban population sizes of metropolises negatively, and the SE correlated positively with the urban population sizes of metropolises in 1990, 2000 and 2006, that is, with urban population sizes getting larger the corresponding PTE was decreasing accordingly, and the SE was increasing consequently and the increasing rate was smaller with the scale increase. Thirdly, the influencing factors of metropolitan efficiency were SE and PTE in 1990 and 2000, respectively. But the PTE became the predominant influencing factor with the rapid expansions of built-up areas and population scales of metropolises in 2006. Fourthly, the Malmquist index results show that the CTE change trends were increasing weakly, the technological change trends were declining, and the TFP change trends were declining obviously during 1990-2006, in which they were all increasing during the sub-period 1990-2000, and all decreasing during the sub-period 2000-2006. Fifthly, the Malmquist index results also demonstrate that the CTE change trend was increasing weakly in the Eastern Coastal China, declining in Central China, and declining evidently in Western China. And with the urban population size increasing the increasing trends of SE became weaker and weaker. And the main causes for the CTE being not too high and its change trends and TFP change trends being increasing weakly lie mainly in the technological degeneracy and PTE change trends declining significantly during 2000-2006. Finally, the analyses show that the China's metropolitan population boom and the rapid spread of built-up area had really caused their resources efficiency losses.