Abacus-based mental calculation (AMC) has been shown to be effective in promoting math ability in children. Given that AMC relies on a visuospatial strategy to perform rapid and precise arithmetic, previous studies mostly focused on the promotion of AMC training on arithmetic ability and mathematical visual-spatial ability, as well as its transfer of advanced cognitive ability. However, little attention has been given to its impact on basic numerical comparison ability. Here, we aim to examine whether and how long-term AMC training impacts symbolic and non-symbolic numerical comparisons. The distance effect (DE) was utilized as a marker, indicating that the comparison between two numbers becomes faster as their numerical distance enlarges. In the current study, forty-one children matched for age and sex were recruited at primary school entry and randomly assigned to the AMC group and the control group. After three years of training, the event-related potential (ERP) recording technique was used to explore the temporal dynamics of number comparison, of which tasks were given in symbolic (Arabic number) or non-symbolic (dot array) format. In the symbolic task, the children in the AMC group showed a smaller DE than those in the control group. Two ERP components, N1 and P2p, located in parietal areas (PO7, PO8) were selected as neural markers of numerical processing. Both groups showed DE in the P2p component in both tasks, but only the children in the AMC group showed DE in the N1 component in the non-symbolic task. In addition, the DE size calculated from reaction times and ERP amplitudes was correlated with higher cognitive capacities, such as coding ability. Taken together, the present results provide evidence that long-term AMC training may be beneficial for numerical processing in children, which may be associated with neurocognitive indices of parietal brain regions.