The existence of minimal length scale has motivated the proposal of generalized uncertainty principle, which provides a potential routine to probe quantum gravitational effects in low-energy quantum mechanics experiment. Hitherto, the tabletop experiment of testing deviations from ordinary quantum mechanics are mostly based on microscopic objects. However, the feasibility of these studies are challenged by the recent study of spacetime quantization for composite macroscopic body. In this paper, we propose a scheme to probe quantum gravity effects by revealing the deviations from predictions of Heisenberg uncertainty principle. Our scheme focus on manipulating the interaction sequences between external laser fields and a single trapped ion to seek evidence of spacetime quantization, therefore reduce the complicity induced by large bodies to some extent. The relevant study for microscopic particles is crucial considering the lack of satisfactory theories regarding basic properties for multi-particles in the framework of quantum gravity. Meanwhile, we are managed to set a new upper limit for deformation parameter.