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For aquaculture wastewater with low ammonium nitrogen concentration, combining the carrier adsorption and biological nitrogen removal processes can maximize their respective advantages. Functional ceramsite that has excellent ammonium nitrogen adsorption performance and excellent biocompatibility was the key to the moving bed biofilm reactor (MBBR) adsorption—shortcut simultaneous nitrification and denitrification (shortcut SND) process. Our group prepared a high-strength lightweight ceramsite that met those requirements. In this study, we applied functional ceramsite in MBBR to cope with low-concentration ammonium aquaculture wastewater. The findings show that utilizing functional ceramsite as a filler was conducive to the adhesion of microorganisms. The biofilm has a minimal effect on the adsorption capacity of ceramsite due to the existence of pores on its surface. Our study further examined the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>NH</mi></mrow><mn>4</mn><mo>+</mo></msubsup></mrow></semantics></math></inline-formula>-N adsorption mechanism of bio-ceramsite. The Freundlich adsorption isotherm model and the quasi-second-order kinetic model had better fitting effects on the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>NH</mi></mrow><mn>4</mn><mo>+</mo></msubsup></mrow></semantics></math></inline-formula>-N adsorption process. The adsorption of bio-ceramsite to <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>NH</mi></mrow><mn>4</mn><mo>+</mo></msubsup></mrow></semantics></math></inline-formula>-N was an endothermic process that included physical and chemical adsorption. Furthermore, the results of adsorption thermodynamics suggested that bio-ceramsite has an affinity for the adsorption of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msubsup><mrow><mi>NH</mi></mrow><mn>4</mn><mo>+</mo></msubsup></mrow></semantics></math></inline-formula>-N. Consequently, this functional ceramsite can be a promising option for MBBR to improve nitrogen removal from aquaculture wastewater.