Cyanobacteria are the most abundant photosynthetic microorganisms， the global distribution of which is mainly regulated by the corresponding cyanophages. A systematic screening of water samples in the Lake Chaohu enabled us to isolate a freshwater siphocyanophage that infects Microcystis wesenbergii， thus termed Mic1. Using cryoelectron microscopy， we solved the 3.5-? structure of Mic1 capsid. The major capsid protein gp40 of an HK97-like fold forms two types of capsomers， hexons and pentons. The capsomers interact with each other via the interweaved N-terminal arms of gp40 in addition to a tail-in-mouth joint along the three-fold symmetric axis， resulting in the assembly of capsid in a mortise-and-tenon pattern. The novel-fold cement protein gp47 sticks at the two-fold symmetric axis and further fixes the capsid. These findings provide structural insights into the assembly of cyanophages， and set up a platform to explore the mechanism of specific interactions and co-evolution with cyanobacteria.