For the screening of novel toxic-element-free and biocompatible electrochemiluminophores, electrochemiluminescence (ECL) of multinary nanocrystals (NCs) was investigated for the first time with Zn-Ag-In-S (ZAIS) NCs as model. Aqueous soluble ZAIS NCs could bring out efficient reductive-oxidation ECL with tri- n-propylamine as coreactant, while coating the ZAIS NCs with a ZnS shell could reduce the surface defects of ZAIS NCs, and enable 6.7-fold enhanced ECL of ZAIS/ZnS NCs as compared to ZAIS NCs. ECL of ZAIS/ZnS NCs was about 4.2-fold that of ternary CuInS2/ZnS NCs, spectrally similar to that of Ru(bpy)32+ with maximum emission around 605 nm, and favorable for less electrochemical interference with a lowered triggering potential (∼0.95 V) than that of Ru(bpy)32+. An ultrasensitive ECL microRNA sensor was fabricated with ZAIS/ZnS NCs as tags, which could sensitively and selectively determine microRNA-141 with a wide linearity range from 0.1 fmol/L to 20 pmol/L and a low limit of detection at 50 amol/L ( S/ N = 3). Multinary NCs might provide a promising alternative to the traditional binary NCs for both electrochemiluminophore screening and NC ECL modulating.