The structural properties and physicochemical characteristics of lotus seed cross-linked resistant starches (LSCSs; LS-0CS, LS-1CS, LS-2CS, LS-4CS, LS-6CS, LS-8CS, LS-10CS, and LS-12CS) with different concentrations of cross-linking agents were investigated. The degrees of cross-linking of LSCSs increased along with the amount of cross-linking agent. The higher the degree of cross-linking, the greater the degree of LSCSs granule agglomeration. The occurrence of the cross-linking reaction was confirmed by the appearance of P = O at 1,250 cm^-1 as assessed by FT-IR, and the covalent bonds formed by the phosphate group in LSCSs were mainly composed of distarch monophosphate (DMSP) as determined by ³¹P NMR. As the crosslinking degree increased, the peak strength of DMSP in starch was stronger and the specific gravity of DMSP was larger. Among the samples, LS-12CS had the highest cross-linking degree, with a greater specific gravity of DMSP. Moreover, the solubility levels of LSCSs decreased and the thermal stability and anti-digestive properties improved as the cross-linking degree increased, which was correlated with the degree of agglomeration and DMSP in LSCSs. The RS content of LS-12CS was 48.95 ± 0.86%.