The use of zero-carbon and carbon-neutral fuels reduces emissions of conventional pollutants, but their emissions can be toxic and have various adverse effects on human health. This article reviews the possible combustion products of zero-carbon and carbon-neutral fuels, as well as their cytotoxic effects and potential health risks. At the same time, the review outlines biological models and toxicity detection methods commonly used in pollutant toxicity studies. Metals, nitrogen oxides (NOX), and ammonia (NH3) emitted from the combustion of metal fuels, hydrogen fuels, and ammonia fuels in zero-carbon fuels are harmful to human health. Exhaust emissions from carbon-neutral fuels, particularly biodiesel, and their blends with gasoline/diesel are cytotoxic, leading to severe cellular damage, such as oxidative damage, inflammatory responses, DNA damage, cell death, or apoptosis. Moreover, the normal function of the human body’s respiratory, cardiovascular, immune, digestive, urinary, and nervous systems may also be impacted by these fuel emissions according to cytotoxic research. Cytotoxicity of fuel combustion products is usually related to the fuel type, time, dose, and cell line used in the experiment. This review provides some ideas for the exhaust emission management of zero-carbon and carbon-neutral fuels and human health assessment. It also presents a theoretical and experimental basis for further research, including in vivo experiments.