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A truly three-dimensional (3D) gas-kinetic flux solver for simulation of incompressible and compressible viscous flows is presented in this work. By local reconstruction of continuous Boltzmann equation, the inviscid and viscous fluxes across the cell interface are evaluated simultaneously in the solver. Different from conventional gas-kinetic scheme, in the present work, the distribution function at cell interface is computed in a straightforward way. As an extension of our previous work (Sun et al., Journal of Computational Physics, 300 (2015) 492–519), the non-equilibrium distribution function is calculated by the difference of equilibrium distribution functions between the cell interface and its surrounding points. As a result, the distribution function at cell interface can be simply calculated and the formulations for computing the conservative flow variables and fluxes can be given explicitly. To validate the proposed flux solver, several incompressible and compressible viscous flows are simulated. Numerical results show that the current scheme can provide accurate numerical results for three-dimensional incompressible and compressible viscous flows.