In situ dynamic testing is conducted to study the dynamic characteristics of the wooden structure of the North House main hall. The velocity response signals on the measurement points are obtained and analyzed using the self-interaction spectral method and stochastic subspace method, yielding natural frequencies, mode shapes, and damping ratios. This study reveals that the natural frequencies and damping ratios are highly consistent between the two methods. Therefore, to eliminate errors, the average of the results from both modal identification methods is taken as the final measured modal parameters of the structure. The natural frequencies of the first and second order in the X direction were 2.097 Hz and 3.845 Hz and in the Y direction were 3.955 Hz and 5.701 Hz. The modal frequency in the Y direction of the structure exceeds that in the X direction. Concurrently, a three-dimensional finite element model was established using ANSYS 2021R1, considering the semi-rigid properties of mortise–tenon connections, and validated based on in situ dynamic testing. The sensitivity analysis indicates adjustments to parameters such as beam–column elastic modulus, tenon–mortise joint stiffness, and roof mass for finite element model refinement. Modal parameter calculations from the corrected finite element model closely approximate the measured modal results, with maximum errors of 9.41% for the first two frequencies, both within 10% of the measured resonant frequencies. The adjusted finite element model closely matches the experimental results, serving as a benchmark model for the wooden structure of North House main hall. The validation confirms the rationality of the benchmark finite element model, providing valuable insights into ancient timber structures along transportation routes.