The invention discloses a method for extracting microalgae lipid through biological enzyme catalysis wall breaking. The method includes the steps that A, a phosphate buffer solution and a biological enzyme catalyst are sequentially added into wet algae mud, or algae slurry, or dry powder or fermentation liquor for culturing harvested lipid-generating microalgae, and the mixture is stirred and heated; B, after the enzyme catalysis degradation reaction is finished, the pH value of a reaction system is adjusted, and the temperature of enzyme catalysis degradation liquid is raised and kept; C, after the reaction is finished, the temperature of the enzyme catalysis degradation system is lowered, an extraction agent is added into the reaction system for lipid extraction, and then demulsifier is added to carry out layering through centrifugation; D, reduced pressure distillation or thin film evaporation concentration is carried out on the oil phase obtained through separation to obtain the microalgae lipid. The method is easy to implement and convenient to operate; due to efficient wall-breaking lipid extraction for the lipid-generating microalgae particularly photoautotroph lipid-generating microalgae, energy input in the microalgae lipid extraction process is reduced, the energy efficiency ratio of microalgae energy is increased, and then comprehensive production cost of microalgae biomass energy is greatly reduced.