Mannose-6-phosphate (M6P) is involved in many metabolic pathways in life, and it has important applications in the treatment of diseases. This study explored a cost-effective enzyme catalytic synthesis method of M6P, using polyphosphate-dependent mannose kinase from Arthrobacter species. This synthesis uses polyphosphate to replace expensive ATP, and it is greener and safer than chemical synthesis. This study investigated the effects of key factors such as metal ions, temperature, and substrate addition on this enzymatic reaction, and improved the conversion efficiency. We moreover take advantage of the response surface method to explore the best catalytic conditions synthetically. The conversion was 99.17% successful under the optimal reaction conditions. After a series of optimizations, we carried out a 200 mL scale-up experiment, which proved that the method has good prospects for industrial applications.