The rapid development of the quantum technology presents huge opportunities for 6G communications. Leveraging the quantum properties of highly excited Rydberg atoms, Rydberg atom-based antennas present distinct advantages, such as high sensitivity, broad frequency range, and compact size, over traditional antennas. To realize efficient precoding, accurate channel state information is essential. However, due to the distinct characteristics of atomic receivers, traditional channel estimation algorithms developed for conventional receivers are no longer applicable. To this end, we propose a novel channel estimation algorithm based on projection gradient descent (PGD), which is applicable to both one-dimensional (1D) and twodimensional (2D) arrays. Simulation results are provided to show the effectiveness of our proposed channel estimation method.