Dynamic self-assembly of iridium complexes in water-soluble nanocontainers is an important bottom-up process for fabricating electrochemiluminescence (ECL) bioprobes. PEGylated apoferritin (PEG-apoHSF) as the host offers a confined space to alter and modify the self-assembly of trans-bis(2-phenylpyridine)(acetylacetonate)iridium(III) [Ir(ppy)2(acac)] based on a pH-dependent depolymerization/reassembly pathway, allowing the formation of ECL-active iridium cores in PEG-apoHSF cavities (Ir@PEG-apoHSF). With an improved encapsulation ratio in PEG-apoHSF, the coreactant ECL behavior of the fabricated Ir@PEG-apoHSF nanodots with tri-n-propylamine (TPrA) was further demonstrated, exhibiting maximum ECL emission at 530 nm that was theoretically dominated by the band gap transition. The application of Ir@PEG-apoHSF as a bioprobe in a "signal-on" ECL immunosensing system was developed based on electroactive Ti3C2Tx MXenes/TiO2 nanosheet (Ti3C2Tx/TiO2) hybrids. Combining with the efficiently catalyzed electro-oxidation of TPrA and Ir(ppy)2(acac) by Ti3C2Tx/TiO2 hybrids, the developed immunosensor showed dramatically amplified ECL responses toward the target analyte of neuron-specific enolase (NSE). Under experimental conditions, linear quantification of NSE from 100 fg/mL to 50 ng/mL was well established by this assay, achieving a limit of detection (LOD) of 35 fg/mL. The results showcased the capability of PEGylated apoHSF to host and stabilize water-insoluble iridium complexes as ECL emitters for aqueous biosensing and immunoassays.