The invention relates to a thermophilic glucoamylase expression cassette and an application thereof. The provided thermophilic glucoamylase expression cassette comprises an aspergillus niger glucoamylase gene 5' flanking region, a thermophilic glucoamylase gene, an aspergillus niger glucoamylase gene 3' flanking region, a promotor, a selective marker gene, a terminator and the aspergillus niger glucoamylase gene 3' flanking region in sequence; the aspergillus niger glucoamylase gene 5' flanking region is selected from at least 1500 DNA fragments at the aspergillus niger glucoamylase gene 5' terminal; the aspergillus niger glucoamylase gene 3' flanking region is selected from at least 1500 DNA fragments at the aspergillus niger glucoamylase gene 3' terminal; and the aspergillus niger glucoamylase gene promotor is arranged in the aspergillus niger glucoamylase gene 5' flanking region. The thermophilic glucoamylase expression vector can generate thermophilic glucoamylase after being introduced in the aspergillus niger.