Plants’ performances are to some degrees dependent on functional traits. Analysis on trait variation that occurs at different levels (or scales) could be an indispensable step towards understanding community assembly and plants’ strategy. Six functional traits were measured in three tropical cloud forests in Hainan Island, China, including leaf area, leaf mass per area, leaf chlorophyll content, leaf thickness, leaf dry weight, and wood density. Trait variations at different organizational scales and taxonomic levels were examined and distinguished by using generalized linear model. From the perspective of organizational scale, we found that trait variations at the interspecific and intraspecific levels were generally stronger than those at the individual or community level; in particular, the interspecific variations of leaf area, leaf mass per area, and leaf dry weight were considerable and accounted for more than half of the total variations. From the taxonomic point of view, we found that plant functional traits generally had stronger variations at species-level than at family- or genus-level, especially in Bawangling. However, variation of woody density was an exception for these tendencies. Our findings demonstrate the multiple sources of trait variations in tropical cloud forests, suggesting that trait-based studies on these forests should not only perform at the species level but also pay attention on the individual-level trait variations.