A finite element model updating method in structural dynamics considering the effects of uncertainty is proposed using interval analysis. Based on the theory of eigen-frequency analysis of structures with interval parameters and the deterministic finite element model updating technologies, an interval model updating formulation are developed by applying the sensitivity method, under the assumption that the variability in measurements and structural parameters as well as the error in the initial finite element model are small. In the iterative formulation, each variable is presented in an interval form which consists of an interval mid-point and an interval radius. Simulation study is conducted by employing a three degrees of freedom mass-spring system and a composite panel, the simulated experimental samples are generated by adopting Latin Hypercube sampling methods. Results show that when the testing samples can accurately reflect the interval characteristics of the experimental modal data, the high convergence accuracy and high efficiency can both be achieved. The presented method provides a solution to the problem that the measured sample is small in finite element model updating of structures with uncertainties.