It has been very difficult to use popular elemental imaging techniques to image Li and B distribution in glass samples with nanoscale resolution. In this study, time‐of‐flight secondary ion mass spectrometry, nanoscale secondary ion mass spectrometry, and atom probe tomography (APT) were used to image the distribution of Li and B in two representative glass samples, and their performance was comprehensively compared. APT can provide three‐dimensional Li and B imaging with very high spatial resolution (≤2 nm). In addition, absolute quantification of Li and B is possible, although there remains room for improving accuracy. However, the major drawbacks of APT include poor sample compatibility and limited field of view (normally ≤100 × 100 × 500 nm3). Comparatively, time‐of‐flight secondary ion mass spectrometry and nanoscale secondary ion mass spectrometry are sample‐friendly with flexible field of view (up to 500 × 500 µm2 and image stitching is feasible); however, lateral resolution is limited to only about 100 nm. Therefore, secondary ion mass spectrometry and APT can be regarded as complementary techniques for nanoscale imaging of Li and B in glass and other novel materials. Copyright © 2016 John Wiley & Sons, Ltd.