Negatively charged Ludox silica nanoparticles (SiNPs) form a complex with atelocollagen (AC) in acidic buffers (pH = 4 or 3). AC is a low-immunogenic derivative of collagen obtained by the removal of N- and C-terminal telopeptide components. Mixed solutions of negatively charged SiNPs and AC were turbid, while positively charged SiNPs (Ludox CL) did not form a complex with AC in pH 4 buffer, indicating that electrostatic attraction is the dominant force to form the complex. Small-angle X-ray scattering (SAXS) and circular dichroism (CD) measurements were made for AC and Ludox LS (or CL) solutions in acetate buffer (pH 4.0) and citrate buffer (pH 3.0). The CD data showed that the stability of the triple helical structure of AC in the buffers is not affected by the complexation. The resulting complex consisting of triple helical AC and SiNPs did not influence the SAXS profile except for the lowest q region investigated. On the contrary, different scattering profiles were observed for the single chain AC and SiNP mixture indicating densely packed SiNPs in the complex. This scattering behavior was fairly explained in terms of the sticky hard sphere model (SHSM). This AC conformation-dependent complexation may be because of the hydrogen bonding interaction between the single chain AC and SiNPs. The temperature-induced change of the complex formation can be applied for thermoresponsive hybrid materials.