The flexure joints are proposed to replace the rigid assembly between the cross-arm and the moving carriages of dual-drive H-type gantry (DHG) for higher reliability and fine rotational alignments. In the literature, the flexure joint of the DHG is modeled as an ideal linear torsional spring, resulting in an inaccurate estimation of the cross-arm’s angle. In this study, a generalized analytical kinetostatic model of flexure-linked DHG is built by considering the geometric nonlinearities. The expressions of beam coefficients in the model are obtained from either beam constraint model (BCM) or Timoshenko BCM (TBCM) according to the given criterion of length-to-thickness ratio. The model is capable to accurately estimate any two variables among the rotation angle of the cross-arm, the misalignment of two carriages, and the net driving force, as long as the other is known. Simulations and experiments on the testbed validate the accuracy and show practical appeals of the proposed model.