We have developed a new particle counting immunoassay system integrated with a resistive-pulse sensor with a low-aspect-ratio pore. The particle counting immunoassay is based on the principle of latex aggregation. The target single-molecule concentration is measured by counting aggregated latex particles that form multimers over the reaction time. To enable highly accurate identification of the number of aggregated particles, we designed and fabricated a low-aspect-ratio pore device to perform quantitative structural analysis of particles. The aggregation numbers of the conjugated particles were classified based on blockade current profiles when the particles translocated through the pore. Time-dependent agglutination reaction monitoring demonstrated that the reaction speed increased for a solution containing a higher concentration of antigens. The results prove the feasibility of using the proposed immunoassay system to count particles while determining the aggregation number based on their current profiles.