Biological system information retrieval system and method thereof disclosed. The biological system information retrieval system may include a query inputting unit, configured for inputting a retrieval query being described to have at least one of a current state and an expected result, a query parsing unit, configured for extracting a token for the current state and the expected result from the retrieval query, and generating at least one of a first corpus data set for the current state and a second corpus data set for the expected result by using the token, and a retrieval requesting unit, configured for inputting at least one of the first corpus data set and the second corpus data set and an option value being generated according to a predetermined syntax to an information management device in order to retrieve a biological system information having similarity.