Clogging is one of the main factors for long-term stable operation of subsurface drainage systems. It also should be paid attention during the application and popularization of subsurface drainage system. The main issues of applying improved subsurface drainage are choosing specifications for filter, preventing clogging, lowering the attenuation of discharge and reducing soil losses. Based on soil column experiment, two filter paving patterns, two kinds of geotextile and three laying locations of the geotextile were considered, the attenuation of discharge process, mass of geotextile clogging and mass of soil losses were simulated under single defense measure of filter or geotextile, and defense measures of filter and geotextile were combined respectively, the reasonable distribution of filter and geotextile for improved subsurface drainage was proposed. The results indicated that Terzaghi critera was reasonable and feasible for choosing specifications of gravel filter and it had good effect on preventing the attenuation of discharge for layered filter and mixed filter. By setting geotextile around the pipe, both layered and mixed filters worked well on slowing down the attenuation of discharge and clogging and soil losses. Furthermore, from the comprehensive view of attenuation of discharge and clogging and soil losses, considering the long-term safe and stable operation of the improved subsurface drainage, priority should be given to the combined measure of layered filter and geotextile around the pipe.