The invention discloses a miniaturization cucumber plant associated protein and a coding gene thereof and an application thereof. An amino acid sequence of the protein is shown as a sequence table 2, which belongs to AAA ATP enzyme family, and is related with microtubule associated protein; the coding gene of the protein has a base sequence shown as a sequence table 1, if the mutation is generated on the base sequence, such as cytosine (C) with 1058 bp bit is substituted by thymidine (T), serine (Ser) with 353 bit for coding the protein is changed to phenylalanine (Phe), the protein inhibits the normal growth of the microtubule cell, the microtubule cytoskeleton is lost, the arrangement is abnormal, concretely, the plant phenotype is plant miniaturization, the height of the mutant plant is about 20% of the height of a normal wild type plant, the fruit length is about 10% of the length of normal wild type fruit, and the leaves and the seeds are obviously shortened. The application of the protein and the coding gene can create condition for cucumber strain-type improvement and cross breeding or exploitation of transgene plants.