The invention provides a communication method of a programmable protocol gateway. The method comprises the steps of S1, setting a plurality of ports; S2, judging the type of serial ports of the programmable protocol gateway, and if the type of the serial ports is an initiative uploading type, executing the S3, and if the type of the serial ports is a polling type, executing the S4; S3, calling a READ port to read data, storing the data into a memorizer, checking the data, and analyzing the data by utilizing the ST language; S4 calling a WRITE port to send data of a preset format in a timing mode, checking the data, calling the READ port to read the data, storing the data into the memorizer, checking the data, and analyzing the data by utilizing the ST language. The invention further provides the programmable protocol gateway and a communication system of an intelligent device with the same. According to the communication method of the programmable protocol gateway, the programmable protocol gateway and the communication system of the intelligent device, a user can convert various protocols into a standard protocol through programming, an upper computer only needs to analyze one protocol, and therefore the programming difficulty is reduced.