The invention relates to a primer pair and a probe used for noninvasive polygene methylation combination detection for early stage colorectal cancer, and includes the primer pair and the probe used for detecting methylation of genes Spetin9, NDRG4, BMP3, THBD and SDC2 and the primer pair and the probe for internal reference ACTB; the sequences of the primer pair and the probe are represented as the SEQ ID No.1 to the SEQ ID No.18. The invention also provides a kit containing the primer pair and the probe and applications thereof. The application method includes free DNA extraction from a plasma specimen, sulfite conversion, PCR amplification reaction, fluorescent signal detection and result determination. The kit and the method are suitable for methylation detection of the five genes Spetin9, THBD, SDC2, NDRG4 and BMP3 in human peripheral blood; compared with a conventional colorectal cancer diagnosis method, the application method fully utilizes the free DNA extraction from a plasma specimen, the DNA methylation and QPCR associated technologies, thus developing the kit having high sensitivity and specificity. The primer pair, probe and kit are used for performing early stage noninvasive screening to human colorectal cancer.