Soil nitrogen (N) and phosphorus (P) shortages limit the growth of shrubs, and P shortage limit the growth of trees in karst ecosystems. Changes in fine root functional traits are the important strategies for plants to respond to such nutrient shortages. However, such responses in karst ecosystems are poorly known. To determine the responses of fine root functional traits to soil N and P changes and define their resource-use strategies in the ecosystem, we tested the specific root length (SRL), root tips over the root biomass (RT/RB), and N concentration (Nroot) in the fine roots of four plant species (two shrubs (Alchornea trewioides and Ligustrum sinense) and two trees (Celtis biondii and Pteroceltis tatarinowii)) during the dry (January) and the wet (July) season. The results showed that the SRL, RT/RB, and Nroot in the fine roots of shrub species were lower than those of tree species, and the three parameters were higher in the wet season than in the dry season. Linear regression models revealed that the SRL, RT/RB, and Nroot of overall species increased with increasing soil N and P concentrations and availabilities, and were positively correlated with increasing rhizosphere soil oxalic acid, microbial biomass carbon (C), and the activities of hydrolytic enzymes. In addition, the individual plant species had unique patterns of the three fine root traits that resulted affected by the change of soil nutrients and biochemistry. Thus, the specific root length, root tips over the root biomass, and N concentrations of fine roots were species-specific, affected by seasonal change, and correlated with soil nutrients and biochemistry. Our findings suggests that fine root functional traits increase the ability of plant species to tolerate nutrient shortage in karst ecosystems, and possibly indicated that a P-exploitative strategy in tree species and an N-conservative strategy in shrub species were exhibited.