Amylopectin with different side chain architecture and distribution were prepared by ɑ-amylase (AM) and maltogenic α-amylase (MA). The purpose of the study was to investigative the effect of molecular entanglement on the anti-thixotropy, gel properties, water distribution and viscosity properties. The results showed that MA specificity hydrolyzed chains ranging from DP 10–17 while retaining the long internal chains, while AM tended to trim the relatively longer chains of DP ≥ 12. The special (ŋsp) in a double-logarithmic plot versus concentration exhibited two linear regions with changes of gradient at AM-M and MA-M polymer concentrations of about 6.20% and 1.31% (w/v), respectively. Higher storage modulus (G′) and final viscosity, and lower frequency dependence indicated the stronger gels of waxy maize starch were formed by MA modification, despite exhibiting a similar thixotropic loop area to AM samples. The microstructure of MA gels showed a more compact honeycomb-like network structure observed by SEM. These results confirmed the chain length profile of the amylopectin pruned by MA was more conducive to produce anti-thixotropic starch-based material. This study is beneficial to provide insights for customizing starch skeleton structure to meet specific industrial application requirements of starch-based products, especially where the rheological properties need to be precisely controlled.