The effective and sensitive detection of the important biomarker, C-reactive protein (CRP), is of great significance in clinical diagnosis. The development of a convenient and highly sensitive electrochemiluminescence (ECL) aptasensor with an immobilized emitter probe is highly desirable. In this work, a probe-integrated ECL aptamer sensor was constructed based on a bipolar silica nanochannel film (bp-SNF) modified electrode for the highly sensitive ECL detection of CRP. The bp-SNF, modified on an ITO electrode, consisted of a dual-layered SNF film, including the negatively charged inner SNF (n-SNF) and the outer SNF with a positive charge and amino groups (p-SNF). The ECL emitter, tris(bipyridine) ruthenium (II) (Ru(bpy)32+), was stably immobilized in a nanochannel of bp-SNF using the dual electrostatic interactions with n-SNF attracting and p-SNF repelling. The amino groups on the outer surface of bp-SNF were aldehyde derivatized, allowing for the covalent immobilization of recognitive aptamers (5′-NH2-CGAAGGGGATTCGAGGGGTGATTGCGTGCTCCATTTGGTG-3′), leading to the recognition interface. When CRP bound to the aptamer on the recognition interface, the formed complex increased the interface resistance and reduced the diffusion of the co-reactant tripropylamine (TPA) into the nanochannels, leading to a decrease in the ECL signal. Based on this mechanism, the constructed aptamer sensor could achieve a sensitive ECL detection of CRP ranging from 0.01 to 1000 ng/mL, with a detection limit (DL) of 8.5 pg/mL. The method for constructing this probe-integrated ECL aptamer sensor is simple, and it offers a high probe stability, good selectivity, and high sensitivity.