In this paper, we consider the decentralized optimization problems with generalized orthogonality constraints, where both the objective function and the constraint exhibit a distributed structure. Such optimization problems, albeit ubiquitous in practical applications, remain unsolvable by existing algorithms in the presence of distributed constraints. To address this issue, we convert the original problem into an unconstrained penalty model by resorting to the recently proposed constraint-dissolving operator. However, this transformation compromises the essential property of separability in the resulting penalty function, rendering it impossible to employ existing algorithms to solve. We overcome this difficulty by introducing a novel algorithm that tracks the gradient of the objective function and the Jacobian of the constraint mapping simultaneously. The global convergence guarantee is rigorously established with an iteration complexity. To substantiate the effectiveness and efficiency of our proposed algorithm, we present numerical results on both synthetic and real-world datasets.