As a barrier to compartmentalize cells, membranes form the interface between a cell and its surroundings. The essential function of a membrane is to maintain a relatively stable environment in the cell, exchange substances selectively and transfer energy and information continually from the outside. It is intriguing that above the phase transition temperature, the membrane lipid molecule will have three modes–lateral diffusion, rotational movement and flip-flop activity. These thermodynamic processes are vital to cell existence, growth, division, differentiation and are also responsible for hundreds of thousands of phenomena in life. Previously, species transport across the membrane was interpreted mainly from a phenomenological view using a lumped system model. Therefore, detailed flow processes occurred in the membrane domain and clues related to life mechanism were not sufficiently tackled. Such important issues can be clarified by modeling nano scale thermal hydrodynamics over the gap space of a cell membrane. Previously observed complex membrane behaviors will be shown in this paper and explained by the thermally induced fluidic convections inside the membrane. A correlation between nano scale hydrodynamics, non-equilibrium thermodynamics and cell membrane activities is set up. The disclosed mechanisms are expected to provide a new viewpoint on the interaction between intracellular and extracellular processes through the membrane.