The invention provides an enhancement type dynamic two-dimensional code authentication system and an authentication method of the enhancement type dynamic two-dimensional code authentication system. A client side of the system at least comprises a data obtaining module, a first operation module and a two-dimensional code generation module, wherein the data obtaining module is used for obtaining user information and payment information, the first operation module is used for combining the above information with a second algorithm to generate a first dynamic password, and the two-dimensional code generation module is used for combining the above information with a first dynamic password to generate two-dimensional information. A server at least comprises a random number generation module, an algorithm reconstitution module, a second operation module and a comparison module, wherein the random number generation module generates a random number according to the user information obtained from the two-dimensional information, the algorithm reconstitution module is used for reconstituting a first algorithm through a preset reconstitution mechanism to generate a second algorithm, the second operation module is used for combining the user information and the payment information with the second algorithm to generate a second dynamic password, and the comparison module compares the second dynamic password with the first dynamic password. The two-dimensional code authentication technology is combined with a brand-new dynamic password authentication technology by the comparison module, a two-dimensional code dynamically changes, and the safety of the two-dimensional code in the authentication process is ensured.