Inspired by the pop-up greeting cards, a 3D collapsible auto-cleaning paper-based electrochemiluminescence (ECL) biosensor (CAPEB) with different functions of signal collection and residual multiple cleaning, is developed for sensitive detection of Ni and Hg by simply regulating its 3D configurations. The multiple fluidic paths and the hollow-channel structure were firstly integrated into the paper substrate, realizing simultaneously repetitive auto-cleaning of the two working electrodes. For achieving ultrasensitive Ni and Hg monitoring, binary catalysis consisting of the intermolecular co-reaction (HO and N-(4-Aminobutyl)-N-ethylisoluminol (ABEI)) and intramolecular catalysis (polyethyleneimine (PEI)-ABEI) was introduced. Specifically, silver nanospheres with a large specific surface area and excellent conductivity were grown on the paper working electrode and served as the sensor substrate for fixing PEI-ABEI and Ni-specific DNAzyme. With the assistance of DNAzyme, CuO-Au and ferrocene (Fc) labeled strand S2 were immobilized on electrode surface through the hybridization reaction, and catalyzed HO to generate reactive oxygen species, promoting the luminescence of ABEI. In the existence of Ni, DNAzyme was activated followed by cleavage of strand S2 to induce the release of Fc, which quenched the ECL signal of ABEI, eventually realizing the detection of Ni. Similarly, for sensitive quantification of Hg, full thymine (T) bases strand S3 was modified on surface of CuO-Au and anchored Hg by T-Hg-T pairing interaction. The ECL intensity was decreased along with increasing of Hg due to the quenching effect of Hg on ECL emission of ABEI. Based on this ingenious system, the detection of Ni and Hg had high sensitivity, wide linear ranges, and low detection limits. The results indicated that the integration of a multi-channel structure into a paper device chips opened new opportunities for designing promising paper-based devices for metal ions diagnosis.