The invention relates to a general miniature programmable controller and a controlling method of the same. The programmable controller comprises a programmable device, a PLC mainframe, 1-4 human-machine interface modules, an extensive module and a CAN bus. The PLC mainframe consists of a flush type microprocessor ARM, an analog quantity input and output module, a digital quantity input and output module, a FLASH memory, a SDRAM memory, an EEPROM memory and an FPGA reconfigurable control algorithm coprocessor, the maximum of a configured I/O point size reaches 256, the maximum of an A/D path number reaches 24, and the maximum of a D/A path number reaches 12. The controlling method is as follows: automatic control of a complicated controlled object is realized, the input and output extensive module flexibly is configured and the computing time of the control algorithm is enabled not to occupy the time for the general miniature PLC to execute program by controlling program initialization, controlling program execution data preparation, controlling program execution and controlling program data transmission steps with intelligent control algorithm compiled in the FPGA.