Salt stress is common but detrimental to plant growth, even in mangroves that live in saline areas. Boron (B) is an essential micronutrient that performs an important role in many functions in plants; however, its protective role under salt stress is poorly understood, especially in long-lived woody plants. In this study, we conducted an indoor experiment under simulated tidal conditions with four treatments (10 parts per thousand salinity, 40 parts per thousand salinity, 40 parts per thousand salinity + 100 mu M B, and 40 parts per thousand salinity + 500 mu M B) and three mangrove species (Avicennia marina, Aegiceras corniculatum, and Bruguiera gymnorrhiza) to investigate the effects of exogenous B on salt tolerance in plant growth, morphology, physiology, and leaf anatomy. The results showed that exogenous low-concentration B treatment (100 mu M B) improved the performance of mangrove species under high salinity stress, especially in terms of physiology and leaf anatomy, while high-concentration B treatment (500 mu M B) had adverse effects. Additionally, we found that the response to exogenous B varied among species in physiology and leaf anatomy, such as proline, malondialdehyde, activity of antioxidant enzymes, palisade tissue, and spongy tissue, which may be related to the salt tolerance of different species. This study may provide useful insights into the alleviation of salt stress by B in mangrove growth and development, which may facilitate mangrove cultivation and afforestation in a saline environment.