A method for secure data transmission and a system using the same method are provided. The method includes: coupling a programmable logic device to a server; receiving a first data packet by the server; inputting the first data packet into a machine learning model to predict a protocol type and a command type of the first data packet by the server; verifying whether the protocol type and the command type are correct by the server; adding the first data packet to a data packet information set in response to the protocol type and the command type being correct by the server; generating a filtering rule according to the data packet information set and deploying the filtering rule in the programmable logic device by the server; and performing the secure data transmission according to the filtering rule by the programmable logic device.