Hamiltonian mechanics plays an important role in the development of nonlinear science. This paper aims for a fractional Hamiltonian system of variable order. Several issues are discussed, including differential equation of motion, Noether symmetry, and perturbation to Noether symmetry. As a result, fractional Hamiltonian mechanics of variable order are established, and conserved quantity and adiabatic invariant are presented. Two applications, fractional isotropic harmonic oscillator model of variable order and fractional Lotka biochemical oscillator model of variable order are given to illustrate the Methods and Results.2 of 23 scholars began to use fractional derivatives to describe the dissipative forces such as frictional forces for the nonconservative systems. Then, fractional calculus of variations was studied by several scholars such as Klimek [27], Agrawal [28,29], Baleanu et al. [30,31], Torres [32], etc. Moreover, the development of the fractional calculus of variations with variable order also made great progress. In [33][34][35], several results for the fractional calculus of variations with variable order were obtained. Particularly, motivated by references [36][37][38], a linear combination of the fractional derivative of variable order was introduced. Based on a combined Caputo fractional derivative of variable order (CCVO), the necessary optimality conditions for variational problems were established [39,40], the fractional variational problem of Herglotz type with variable order was studied [41], and two fractional isoperimetric problems and a new variational problem subject to a holonomic constraint were presented [42].After differential equations of motion are established through the calculus of variations, the next task is to find the solutions to them in dynamics. In fact, the solution to the equations can be given if one can find all of the integrals of the equations. An integral is a conserved quantity; therefore, people try their best to find all of the conserved quantities of a mechanical system. By means of the analysis of forces, Newtonian mechanics gives three conservation laws, i.e., the conservation of momentum, the conservation of mechanical energy, and the conservation of moment of momentum. By means of the analysis of the form of Lagrangian, Lagrangian mechanics gives two conservation laws, i.e., the conservation of generalized energy and the conservation of generalized momentum. The conservation of generalized momentum may be a conservation of momentum, a conservation of moment of momentum, or neither. The physical meaning of the conservation law in Lagrangian mechanics is less clear than that in Newtonian mechanics, whose three conservation laws have very clear physical meaning. However, the conserved quantities deduced by Lagrangian mechanics are more than those deduced by Newtonian mechanics. Since German mathematician Emmy Noether published her famous paper [43], the Noether symmetry method has become a modern method for seeking the conservation law of mechanical systems (see...