In this work, a comparative study on the supramolecular assemblies formed by calixpyridinium and two alginates with different viscosities was performed. We found that sodium alginate (SA) with medium viscosity (SA-M) had a better capability to induce aggregation of calixpyridinium in comparison with SA with low viscosity (SA-L) because of the stronger electrostatic interactions between calixpyridinium and SA-M. Therefore, the morphology of calixpyridinium-SA-M supramolecular aggregates was a compact spherical structure, while that of calixpyridinium-SA-L supramolecular aggregates was an incompact lamellar structure. As a result, adding much more amount of 1,3,6,8-pyrenetetrasulfonic acid tetrasodium salt to calixpyridinium-SA-M solution was required to achieve the balance of the competitive binding, and in comparison with calixpyridinium-SA-L supramolecular aggregates, calixpyridinium-SA-M supramolecular aggregates were more sensitive to alkali. However, for the same reason, in comparison with calixpyridinium-SA-M supramolecular aggregates, calixpyridinium-SA-L supramolecular aggregates were much more stable in water not only at room temperature but also at a higher temperature, and even in salt solution. Therefore, in comparison with calixpyridinium-SA-L supramolecular aggregates, calixpyridinium-SA-M supramolecular aggregates exhibited a completely opposite response to acid because of the generation of salt. Because SA is an important biomaterial with excellent biocompatibility, it is anticipated that this comparative study is extremely important in constructing functional supramolecular biomaterials.