Abstract Experiments that study complex real world systems in business, engineering and sciences can be conducted at different levels of accuracy or sophistication. Nested space-filling designs are suitable for such multi-fidelity experiments. In this paper, we propose a systematic method to construct nested space-filling designs for experiments with two levels of accuracy. The method that makes use of nested difference matrices can be easily performed, many nested space-filling designs for experiments with two levels of accuracy can thus be constructed, and the resulting designs achieve stratification in low dimensions. In addition, the proposed method can also be used to obtain sliced space-filling designs for conducting computer experiments with both qualitative and quantitative factors.