The boundary layer height (BLH) distinguishes the interface between the lower and free atmosphere, which is a key variable in numerical simulation, aerosol, and environmental pollution studies. Thus, the goal of this work is to propose a novel method conjuncting with numerical regularization to analyze climate characteristics of the marine boundary layer height (MBLH) using 2007-2011 GPS-RO data from the COSMIC mission. While traditionally, the difference method has been used to achieve this aim, herein, we propose an innovative method, in which the bending angle profile gradient was calculated using the numerical regulation method where the regulation parameters are determined by the double-parameter model function method. Then, the MBLH was determined by employing the maximum gradient method to ascertain the height corresponding to the smallest gradient. The results show a correlation between currents and the MBLH—a relationship that has not been previously demonstrated. A low MBLH is associated with seasons and regions where cold ocean currents are prevailing; whereas a high MBLH is observed in the seasons and places where warm currents are prevailing. This correlation was validated by comparing the obtained results with different occultation data—i.e., atmprf and echprf—which also established that atmprf is more sensitive to convective cloud top capture. In seas with active convection, the armprf calculated bending angle is higher than that from echprf. Subsequently, the standard deviation was used to express the MBLH confidence level. The results show that the MBLH standard deviation is highest in low latitudes and lowest in the middle and high latitudes. Furthermore, we analyzed the interannual MBLH variation trend, which displayed a seasonal variation and spatial distribution corresponding with the current and subsolar point. Finally, we conducted a case study in the South China Sea, and identified a distinctive seasonal change and downward trend.