Covalent organic frameworks (COFs) are new emerging functional porous materials. Strong covalent bonds result in molecular building blocks that can be arranged in layered two-dimensional (2D) or three-dimensional (3D) periodic networks. However, to the best of our knowledge, there have been no reports on experimental and theoretical studies of thermoelectrical properties of COFs to date. Therefore, density functional theory (DFT) and the Boltzmann transport equation have been applied in this work to calculate the semiclassical transport coefficients for phthalocyanine (Pc)-based NiPc, NiPc-benzothiadiazole (BTDA), and Pc COFs. Owing to the well-ordered stacking of the phthalocyanine units and linkers in these compounds, charge-carrier transport is facilitated in the stacking direction. In all studied compounds, the highly directional character of π-orbitals provides band-structure engineering and produces a type of low-dimensional hole transport along the stacking direction. All studied compounds are indirect semiconductors. The low-dimensional transport of holes and the localized states in both valence and conduction bands prevent the electron–hole compensation effect in the Seebeck coefficients, correlating with the large Seebeck coefficients of the studied compounds. Insertion of the electron-deficient building block benzothiadiazole in the NiPc-BTDA COF leads to positive Seebeck coefficients along the a-, b-, and c-directions. The relaxation time was estimated in our investigations from DFT band-structure calculations and the experimentally defined mobility, leading to determination of the electrical conductivity and electronic contribution to the thermal conductivity, as well as figure of merit (ZT) estimation. Ni atom provided greater electrical conductivity along the c-direction in comparison with metal-free Pc COF, and NiPc COF showed the highest thermoelectric performance among the studied COFs.