A new method combined with using single-point settlement gauges and strain gauges was developed to monitor the compression deformation of pile foundation，the compressions of pile shafts and soil layers beneath the pile bottom. The measurement depth of the new-developed method can reach more than 100 m below the ground surface，which effectively replenished the settlement monitoring technology of super-long pile foundations in the deep soft soil. The compression deformation behaviors were then systematically analyzed by field experimental and numerical methods. The main conclusions show that the vertical compression deformation of the pile foundation increaseds in a ladder shape during the construction of the bridge，and the post-construction settlement is approximate to 5.0 mm，which is less than the normative limit （20 mm） of a related design code； small deformation of the pile foundation cap may lead to differences in the settlements and axial forces of piles at different positions； then，the total compression deformations as well as the unit compression of the subsoil layers within 20~30 m below the pile bottom are quite small，hence it can be preliminarily determined that the influencing thickness of the compressible layers below the bottom of super-long pile foundations of high-speed railways in this tested area is approximate to 20 m； moreover，the accuracy of pile compression measured by settlement gauges is generally higher than that measured from strain gauges，and the pile compression can take a proportion as large as 30%~40% of the total pile settlement for a super-long pile foundation，hence it should be considered in calculating the pile foundation settlement； in addition，negative friction resistance appearis in the shallow depth，and there is a neutral plane at 11 m below the top of the pile； furthermore，the position of the neutral plane gradually moves up with the increase of the pile foundation loads.