In order to improve the separation efficiency of the downhole separator in injecting the hollow glass spheres(Referred to as HGS) for variable gradient managed pressure drilling(Referred to as MPD), and accurately grasp the distribution law of wellbore pressure, the new type of downhole filter separator with spherical filter plug and metal filter screen as the core structure were developed in this paper, and its overall structure and working principle were expounded. The filter structure was simulated by the porous media model, and Euler multiphase flow model was used to simulate the flow process of the mixed fluid of drilling fluid and HGS in wellbore, and then the influence of injection rates of different fluid or volume fraction of HGS on the separation efficiency of the filter separator was analyzed by numerical simulation. The sensitivity experiment of the separation efficiency of the filter separator was carried out under different influencing factors, such as pump flow rate, density, volume fraction and diameter of HGS based on the self-developed laboratory simulation experiment system for variable gradient MPD. According to the separation efficiency obtained from numerical simulation and laboratory experiments, and considering the energy exchange between the wellbore and the formation as well as the influence of the wellbore temperature and pressure on the physical parameters of the fluid, a transient model of the coupled wellbore temperature-pressure under the single-phase flow condition for variable gradient managed pressure drilling in deep water was established. The finite difference and Gauss-Seidel iteration methods were used to discretize and solve the model respectively, and the sensitivity analysis of distribution law for the wellbore pressure under the condition of HGS volume fraction or density, the position or number of the filter separator was carried out. The study results showed that the new downhole filter separator can significantly improve the separation efficiency, of which the maximum value can be up to 98.5%. Compared to the conventional drilling, the annulus pressure presents an obvious inflection point at the position of the filter separator, the overall distribution is in the shape of a broken line, and the position and number of the inflection point change synchronously with the position and number of the separator under the condition of variable gradient MPD. The wellbore pressure was negatively correlated the depth from the filter separator to wellhead or the HGS volume fraction, and positively correlated with the HGS density or pump flow rate. This results can provide a theoretical reference for the further development of the variable gradient managed pressure drilling method in deep water.