Microcystins (MCs) produced by
Microcystis aeruginosa
are harmful to animal and human health, and there is currently no effective method for their removal. Therefore, the development of biological approaches that inhibit cyanobacteria and remove MCs is needed. We identified strain MB1, confirmed as
Morchella
, using morphological and molecular evolution methods. To assess the impact of strain MB1 on
M. aeruginosa
, we conducted an experiment in which we inoculated
M. aeruginosa
with
Morchella
strain MB1. After their co-cultivation for 4 d, the inoculation with 0.9696 g MB1 completely inhibited and removed
M. aeruginosa
while concurrently removing up to 95% of the MC content. Moreover, within 3 d of their co-cultivation, MB1 removed more than 50% of nitrogen and phosphorus from the
M. aeruginosa
solution. Therefore, the development of effective biological techniques for MC removal is paramount in safeguarding both the environment and human well-being. We herein successfully isolated MB1 from its natural habitat. This strain effectively inhibited and removed
M. aeruginosa
and also reduced the content of nitrogen and phosphorus in the
M. aeruginosa
solution. Most importantly, it exhibited a robust capability to eliminate MCs. The present results offer a new method and technical reference for mitigating harmful algal blooms.