CuFe2O4 magnetic nanocrystal clusters (CuFe2O4 MNCs) was proposed as a new matrix for small molecule analysis by negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the first time. We demonstrated its advantages over conventional organic matrices in the detection of small molecules such as amino acids, peptides, nucleobases, fatty acids, and steroid hormones. A systematic comparison of CuFe2O4 MNCs with different ionization modes revealed that MS spectra obtained on CuFe2O4 MNC matrix in negative ion mode was only featured by deprotonated ion peaks with free matrix background, which was different from the complicated alkali metal adducts produced in positive ion mode. The developed method was found relatively tolerant to salt contamination and good reproducibility. Detection limit down to subpicomolar level was achieved when testosterone was analyzed. In addition, by comparison of the MS spectra obtained from bare Fe3O4 and MFe2O4 MNC (M = Co, Ni, Cu, Zn) matrices, two main factors of MFe2O4 MNC matrices were unveiled to play a vital role in assisting negative ion desorption/ionization (D/I) process: doping transition metals into ferrite nanocrystals favoring laser absorption and energy transfer; good match between the UV absorption of MFe2O4 MNCs and the excitation of nitrogen laser source facilitating LDI efficiency. This work creates a new application branch for MFe2O4 MNCs and provides an alternative solution for small molecule analysis.