Learning 3D graph with spatial position as well as node attributes has been recently actively studied, for its utility in different applications e.g. 3D molecules. Quantum computing is known a promising direction for its potential theoretical supremacy for large-scale graph and combinatorial problem as well as the increasing evidence for the availability to physical quantum devices in the near term. In this paper, for the first time to our best knowledge, we propose a quantum 3D embedding ansatz that learns the latent representation of 3D structures from the Hilbert space composed of the Bloch sphere of each qubit. Specifically, the 3D Cartesian coordinates of nodes are converted into rotation and torsion angles and then encode them into the form of qubits. Moreover, Parameterized Quantum Circuit (PQC) is applied to serve as the trainable layers and the output of the PQC is adopted as the final node embedding. Experimental results on two downstream tasks, molecular property prediction and 3D molecular geometries generation, demonstrate the effectiveness of our model. We show the capacity and capability of our model with the evaluation on the QM9 dataset (134k molecules) with very few parameters, and its potential to be executed on a real quantum device.