A method for preparing a linoleic acid sustained-release algal inhibiting agent comprises the following steps that firstly, linoleic acid is dissolved through ethyl oleate, emulgator is added into the linoleic acid, and the emulsified linoleic acid is added into a solution of sodium alginate tech grade; secondly, the solution obtained in the first step is dropwise added into a glacial acetic acid solution containing chitosan and calcium chloride to form microspheres; thirdly, after the microspheres are cooled to the indoor temperature, a cross-linking agent is added into the cooled microspheres; fourthly, the process of suction filtration is carried out, and the microspheres to which the cross-linking agent is added are washed by petroleum ether and distilled water; fifthly, the linoleic acid sustained-release algal inhibiting agent is obtained after drying. Algal inhibition effective time is prolonged, the algal inhibition effect is improved, and cost is reduced. All adopted preparing materials are natural polymer materials which are non-toxic, good in biocompatibility and biodegradable, and the problems of secondary pollution caused by chemical algal removing and bio-concentration and biological amplification caused by chemical medicines can be effectively avoided.