The canonical transformation and Poisson theory of dynamical systems with exponential, power-law, and logarithmic non-standard Lagrangians are studied, respectively. The criterion equations of canonical transformation are established, and four basic forms of canonical transformations are given. The dynamic equations with non-standard Lagrangians admit Lie algebraic structure. From this, we establish the Poisson theory, which makes it possible to find new conservation laws through known conserved quantities. Some examples are put forward to demonstrate the use of the theory and verify its effectiveness.