The invention provides an intelligent programmable axial plunger pump controller and a control method, and belongs to the field of intelligent hydraulic elements. The controller comprises a sensor group, a control panel, and an ARM chip, an RISC-V chip, a signal acquisition module, a filtering module, a charge amplifier, a power amplifier, a mode selection module, a display module and a cloud storage module which are installed on the control panel; and the control panel is further provided with a plurality of external interfaces. The magnitude of flow in a variable piston cavity of a hydraulic pump and the swing angle of a swash plate can be controlled by the ARM chip; automatic compound control over the pressure, flow and power of the axial plunger pump is achieved; meanwhile, the pressure, flow and power of the axial plunger pump can be controlled by detecting signals such as the outlet pressure of the hydraulic pump, the swing angle of the swash plate and vibration on a pump shell; the state of the hydraulic pump is monitored and recognized based on the RISC-V chip, common faults of the hydraulic pump are judged, and judgment results are transmitted to the ARM chip, thus implementing predictive maintenance of the hydraulic pump.