In order to find out the bearing behavior of super-long piles located in deep soft clay over stiff layers around Dongting Lake, China, a test pile was first designed with the field loading test finished afterward. Based on the measured test results, load transfer mechanism and bearing behavior of the pile shaft were discussed in detail. Then, by introducing a bi-linear model for shaft friction and the tri-linear model for pile tip resistance, respectively, the governing differential equation of pile-soil system was set up by the load transfer method with the analytical solutions derived as well, taking into account the effect by stratified feature and various bearing conditions of subsoil, material nonlinearity, and the sediment under pile tip. Furthermore, formulas to determine the axial capacity of super-long piles by the pile top settlement were advised and applied to analyze the test pile. Good agreement between the predicted load-settlement variations and the measured data is obtained to verify the validity of the present method. The results also show that, the axial bearing capacity of super-long piles should be controlled by the allowable pile top settlement, and buckling stability of the pile shaft should be paid attention as well.