In this paper, low-cost counter electrodes (CEs) based on water-soluble multiwall carbon nanotube (MWCNT) and Cu2ZnSnSe4 nanoparticle (CZTSe NP) composites have been successfully introduced into a quantum dot-sensitized solar cell (QDSC) system. Suitable surface modification allows the MWCNTs and CZTSe NPs to be homogeneously dispersed in water, facilitating the subsequent low-temperature spray deposition of high quality composite films with different composite ratios. The electrochemical catalytic activity of the composite CEs has been critically compared by electrochemical impedance spectroscopy and Tafel-polarization analysis. It is found that the composite CE at the MWCNT : CZTSe ratio of 0.1 offers the best performance, leading to an optimal solar cell efficiency of 4.60%, which is 50.8% higher than that of the Pt reference CE. The as-demonstrated higher catalytic activity of the composite CEs compared to their single components could be ascribed to the combination of the fast electron transport of the MWCNTs and the high catalytic activity of CZTSe NPs.