The deactivation of bifunctional Ni/HZSM-5 catalysts is essentially due to the formation of heavy secondary products (i.e., coke) in the hydrodeoxygenation (HDO) of bio-oil. Coke deposited on the Ni/HZSM-5 catalyst was characterized using analytical techniques, including Fourier transform infrared spectroscopy (FTIR), thermogravimetric (TG) analysis, and transmission electron microscopy (TEM). The type and quantitative distribution of the deposited coke on the Ni/HZSM-5 catalyst were determined by the dissolution of the aluminum-silicate matrix in a hydrofluoric acid solution. The composition of soluble coke was obtained by gas chromatography-mass spectrometry (GC-MS) measurements. It is found that coke can be divided into soft coke, hard coke, and graphite at different reaction temperatures. Organic reactants can be transformed into soft coke and hard coke by different chemical reactions, such as alkylation, aromatization, hydrogen transfer, and dehydrogenation. The quantitative distribution between soluble and insoluble coke on the Ni/HZSM-5 catalyst in the HDO of bio-oil and the related kinetic characteristics of coke were presented in the paper.