The invention discloses a security coordinate transmission method. The method comprises the following steps: a pipeline facility security coordinate collected in site and a mapping control point result table are stored in sending security equipment; the sending security equipment computes a relative relation of two pieces of data and transmits the relative relation to sending intermediate equipment through a sending security U disk; the sending intermediate equipment receives the relative relation data and transmits the same to a sending non-security U disk; the sending non-security U disk receives the relative data and sends the same to the internet; receiving non-security equipment receives the relative relation data and transmits the same to receiving intermediate equipment through a receiving non-security U disk; the receiving intermediate equipment receives the relative relation data and transmits the same to the receiving security equipment through a receiving security U disk; the receiving security equipment receives the relative relation data and computes together with the mapping control point result table stored in the receiving security equipment to relieve the relativerelation, thereby acquiring the pipeline facility security coordinate collected in site. The invention further provides a security coordinate transmission system and a system use method thereof. The security coordinate transmission method disclosed by the invention has the advantages of being fast in transmission speed and safe in data transmission.