Plant innate immunity mainly includes the recognition of conserved pathogen-(or microbial) associated molecular patterns (P/MAMPs) by pattern recognition receptors (PRRs), and the recognition of highly variable effectors by highly polymorphic resistance (R) proteins. There is a wide range of signal molecules exchange and recognition between plants and pathogens. Small molecule compounds affect the signal regulation in plants and their pathogens, which decided the outcome of the competition between them to a large extent. Illustrating these signaling molecules and exploring their interaction between plant and pathogen will help to reveal the mechanism of plant disease resistance and to explore new genes related to plant disease resistance. Reported studies have identified these signal molecules and their roles in the interaction between plants and pathogens. Our review summarizes the process of signal molecules and mechanisms between plant and pathogen interactions, the occurrence and signal transduction caused by PAMP-triggered immunity (PTI) and Effector-triggered immunity (ETI), and the downstream signal molecules and signal transduction. We also indicate future research needs.