This disclosure relates to method and system for generating cognitive security intelligence for detecting and preventing malwares. In one embodiment, the method includes monitoring instructions being executed by a processor of a computing system, determining events triggered and activities performed by the execution of the instructions, correlating the events and the activities to determine a sequence of events and activities, and mapping the sequence of events and activities with a topographical threat map to detect a pattern match corresponding to a malware. The topographical threat map is event and activity behavior map of a number of categories of malwares, and is built based on a cognitive analysis using deep learning which may also be enriched with external knowledge or historic knowledge. The method further includes effecting a remedial measure, upon detecting the pattern match, to prevent the malware by constructing remedial instructions to be executed by the processor.