The invention discloses a method and apparatus for controlling combustion of engine having a mixed combustion mode. The method of controlling combustion of an engine improves unstable ignition and knocking which may be generated in an engine to which a diesel-gasoline mixed combustion mode and a gasoline mixed combustion mode are applied to low load and high load driving zones. The method includes: determining a combustion mode according to a current driving state of the engine; determining a compression ratio corresponding to the combustion mode; controlling a variable compression ratio device to control a compression ratio of a cylinder; determining whether the combustion state of the engine obtained during the combustion after the control to the compression ratio satisfies a set condition; and performing a compression ratio compensation such that the combustion state of the engine satisfies the set condition with taking a combustion pressure sensor signal as a feedback signal when the set condition is not satisfied.