To address the challenges of high-dimensional channel estimation and underutilized spatial correlations among users in holographic MIMO (HMIMO) systems, this paper proposes a joint graph-cut algorithm for multi-user channel estimation in the wavenumber domain. The size of the conventional angular domain channel matrix increases with the number of antennas in densely-spaced HMIMO. Therefore, user channels are projected into the wavenumber domain via a Fourier harmonic transform, revealing their inherent clustered sparsity and exploiting common scatterer clusters among users. Subsequently, a joint graph-cut channel estimation (JGC-CE) algorithm based on multi-user common supports is designed. In each iteration, the algorithm first partitions user clusters to extract shared supports. Then for each user, it performs users' individual graph update and channel estimation to reconstruct the channel matrix. Simulation results demonstrate that the proposed method outperforms independent estimation schemes for individual users in accuracy while reducing pilot length.