Boron is a naturally occurring trace chemical element. High concentrations of boron in nature can adversely affect biological systems and cause severe pollution to the ecological environment. We examined a method to effectively remove boron ions from water systems using sugarcane bagasse biochar from agricultural waste with NH3 nanobubbles (10% NH3 and 90% N2). We studied the effects of the boron solution concentration, pH, and adsorption time on the adsorption of boron by the modified biochar. At the same time, the possibility of using magnesium chloride and NH3 nanobubbles to enhance the adsorption capacity of the biochar was explored. The carbonization temperature of sugarcane bagasse was investigated using thermogravimetric analysis. It was characterized using XRD, SEM, and BET analysis. The boron adsorption results showed that, under alkaline conditions above pH 9, the adsorption capacity of the positively charged modified biochar was improved under the double-layer effect of magnesium ions and NH3 nanobubbles, because the boron existed in the form of negatively charged borate B(OH)4− anion groups. Moreover, cations on the NH3 nanobubble could adsorb the boron. When the NH3 nanobubbles with boron and the modified biochar with boron could coagulate each other, the boron was removed to a significant extent. Extended DLVO theory was adopted to model the interaction between the NH3 nanobubble and modified biochar. The boron adsorption capacity was 36 mg/g at room temperature according to a Langmuir adsorption isotherm. The adsorbed boron was investigated using FT-IR and XPS analysis. The ammonia could be removed using zeolite molecular sieves and heating. Boron in an aqueous solution can be removed via adsorption with modified biochar with NH3 nanobubbles and MgCl2 addition.