We design and develop a high-performance magnetic shielding system for a long baseline fountain-type atom interferometer. The shielding system is achieved by a combination of passive shielding using permalloy and active compensation with coils. An 11.4 m-long three-layer cylindrical shield is completed by the process of welding, local annealing, and entire annealing. The active compensations compress the residual magnetic field to 8.0 nT max-to-min and the corresponding gradient below 30 nT/m over 10 m along the axial direction in which external compensation, internal compensation, and constant magnetic field (C-field) compensation reduce the inhomogeneities to 25.0, 12.6, and 1.7 nT (standard deviation) sequentially. We estimate that this system could reduce the systematic error of the quadratic Zeeman shift to the 10-13 level for the weak equivalence principle test with a simultaneous 85Rb-87Rb dual-species atom interferometer.