The improvement of electrochemiluminescence (ECL) performance relies on the electron transfer efficiency between luminophore and coreactant. An ultrasensitive ECL micro-reactor with confinement-enhanced performance was prepared by using the covalent organic framework-LZU1-functionalized metal-organic framework (MOF@COF-LZU1) as a platform to assemble enormous N,N-dibutyl-2-hydroxyethylamine (DBAE) and tris(4,4′-dicarboxylic acid-2,2′-bipyridyl) ruthenium(II) [Ru(dcbpy)32+] into its pore channels. Compared to individual substances of γ-CD-MOF and COF-LZU1, the synergistic effects can conduce to the enhancement of the intensity, durability and sensitivity of the micro-reactor. Besides, COF-LZU1 can provide a mild environment to accommodate a certain amount of DBAE by concentrating them from the aqueous solution into its hydrophobic cavities and boost the oxidation efficiency of DBAE to generate more DBAE●+ and profited the survival of DBAE●, leading to an improved reaction efficiency with the Ru(dcbpy)32+ intermediate. Thanks to the confinement-enhanced strategy, engineered as high-functioning luminescent materials, Ru@γ-CD-MOF@COF-LZU1 micro-reactors decorated with Au NPs can facilitate electron transfer and capture primary antibodies (Ab1). Moreover, Au–Pd–Pt noble metal aerogels (NMAs) functionalized MoS2 NFs (Au–Pd–Pt NMAs@MoS2 NFs) were chosen as base material due to its large specific surface areas, high porosity, and excellent electrical conductivity. Based on above merits, the sensor demonstrated a sensitive response to CYFRA 21-1 detection in a linear concentration gradient from 10 fg/mL to 50 ng/mL with a detection limit of 0.0055 pg/mL (S/N = 3). The COF-LZU1 decorated ECL micro-reactors were constructed based on the signal amplification strategies to realize accurate CYFRA 21-1 detection.