The reinforcing behaviors of siliceous earth (SE) nanoparticles and silica on natural rubber (NR) were compared. SE employed in this work was formed by volcanic eruptions 100 million years ago and mainly consists of SiO2 (∼80%), Al2O3 (∼14%), and K2O (∼4%) and is composed of low quartz and illite in crystal structure and with a special flaky and laminated morphology. The effects of SE slurry with different filler loading of 30, 40, 50 per hundred parts of rubber (phr), and 40 phr silica(S-40) were investigated. Mechanical properties were measured, and the results show that 300% modulus, elongation at break, tensile, and tear strength of SE/NR are all higher than those of S-40. Combination results of tensile properties and rubber process analyzer (RPA), the rubber–filler interaction parameter (I) was calculated and the results show the value of I increase slightly with SE loading, while obviously higher than that of S-40. But the results of dynamic mechanical analysis and bound rubber content show that S-40 has obviously lower tan δ and higher bound rubber content, which indicate that there exists stronger rubber–filler interaction between silica and NR. The seemingly conflicting results imply that the effect of the two fillers on the NR network structure should be different. The special morphology of SE can help them to distribute more evenly in the NR matrix, making it less likely to form particle networks and providing very strong filler–rubber interaction, while showing higher average rubber–filler interaction and results in better mechanical properties of SE/NR composites.