The invention discloses a depth message detection method based on a network isolation apparatus. The method comprises the following steps of step1, according to a type of input messages, filtering the input messages and acquiring an IP message; step2, carrying out first depth message detection on an option of a head portion of the IP message; if the option does not pass through the detection, discarding the messages; and if the option passes through the detection, entering into a step3; step3, according to a protocol type in the head portion of the IP message, filtering the messages and acquiring a TCP/UDP message; step4, according to a safe strategy configured by the isolation apparatus, carrying out legality detection on the messages; if the messages do not pass through the detection, discarding the messages; if the messages pass through the detection, entering into a step5; step5, carrying out second depth message detection on an option of a head portion of the TCP message, if the option does not pass through detection, discarding the messages; and if the option passes through the detection, entering into a step6; step6, carrying out network layer protocol peeling on the messages; step7, sending the peeled messages to an opposite side through an isolation island; and step8, carrying out network layer protocol packaging on the message again and sending to a corresponding network. An isolation degree of the apparatus is increased.