The invention discloses a method for removing thalline cells from a thermal gel broth and belongs to the field of bioengineering. In the thermal gel broth, the microbial thalline is wrapped in insoluble thermal gel and they are hard to separate from each other. The product is a high-quality thermal gel product with low nitrogen content at the industrial scale, and the microbial thalline needs to be separated and removed. By treating the solid after first filter pressing of the thermal gel broth, the solid is dissolved in an alkaline solution, and then insoluble colloids therein are completelydissolved by a homogenization method. Neutral red and aniline blue are adopted for dyeing and microscopic examination and detection so as to ensure that there is no insoluble colloids after the alkalidissolution. Subsequent filter pressing rate and bacterial eliminating rate can be significantly increased, and then quality of the thermal gel final product is improved at the industrial scale.