The fruit fly, Drosophila melanogaster, is able to discriminate visual landmarks and form visual long-term memory in a flight simulator. Studies focused on the molecular mechanism of long-term memory have shown that memory formation requires mRNA transcription and protein synthesis. However, little is known about the molecular mechanisms underlying the visual learning paradigm. The present study demonstrated that both spaced training procedure (STP) and consecutive training procedure (CTP) would induce long-term memory at 12 hour after training, and STP caused significantly higher 12-h memory scores compared with CTP. Label-free quantification of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and microarray were utilized to analyze proteomic and transcriptomic differences between the STP and CTP groups. Proteomic analysis revealed 30 up-regulated and 27 down-regulated proteins; Transcriptomic analysis revealed 145 up-regulated and 129 down-regulated genes. Among them, five candidate genes were verified by quantitative PCR, which revealed results similar to microarray. These results provide insight into the molecular components influencing visual long-term memory and facilitate further studies on the roles of identified genes in memory formation.