Quercus species (Fagaceae) are widely distributed from temperate to tropical forests in the northern hemisphere and can grow well at both karst and non-karst habitats. Revealing the differences in plant functional traits of deciduous Quercus species commonly growing at karst and non-karst habitats is critical to understand their underlying adaptive mechanisms and can provide scientific basis for the selection of tree species in karst vegetation restoration practice. In this study, 13 plant functional traits including stomatal size (SZ), stomatal length (SL), stomatal density (SD), and stomatal pore index (SPI) at the cellular scale, leaf thickness (LT), thickness of adaxial epidermis (AD), thickness of abaxial epidermis (AB), and palisade mesophyll thickness to leaf thickness ratio (PTR) at the tissue scale, specific leaf area (SLA), and leaf dry matter content (LDMC) at the leaf scale, non-structural carbohydrates (NSC), leaf construction cost (LCC) and intrinsic water-use efficiency (iWUE) at the whole-plant scale of three deciduous Quercus species, i.e., Q. variabilis, Q. acutissima and Q. fabri growing at both karst and non-karst habitats in Guangdong Province were determined and compared. The correlations of the 13 plant functional traits with local climatic and edaphic variables were detected, too. The results showed that: 1) habitat was the main contributor to the variation of the studied functional traits except for AD and LDMC of the studied deciduous Quercus species; the traits of SPI, LT, AB, PTR, SLA, NSC, LCC and iWUE were significantly different between karst and non-karst habitats, and the differences were species-dependent; 2) at both habitats, the traits at the leaf scale were significantly correlated with mean annual precipitation; but at karst habitat, the traits at the cellular, tissue and whole-plant scales were significantly correlated with mean annual precipitation, mean annual temperature, soil total nitrogen, phosphorus contents and soil pH, while at non-karst habitat, those traits were significantly correlated with only mean annual precipitation, mean annual temperature, soil total nitrogen, and phosphorus contents; 3) the correlations among the 13 plant functional traits were more complex at karst habitat than those at non-karst habitat, with significance existing in SPI-SD, AD-NSC, PTR-NSC, SLA-LCC and AB-iWUE at karst habitat, while only in SLA-LCC and AB-iWUE at non-karst habitat, indicating the trade-offs of functional traits at different biological scales of the deciduous Quercus species for the adaptation to karst habitat. The results also imply Q. variabilis can be preferentially adopted for vegetation restoration due to its greater variability in plant functional traits than Q. acutissima and Q. fabri when growing at kart habitat.