The invention discloses a paraffin hydrocarbon shape selective isomerization catalyst, a preparation method and application thereof. The catalyst comprises a rare earth-modified molecular sieve and a halogen-modified inorganic melting-resisting oxide and at least one VIII-family precious metal, wherein the molecular sieve is a TON type molecular sieve, the weight ratio of the rare earth-modified molecular sieve to the halogen-modified inorganic melting-resisting oxide is 10:90-90:10, in the catalyst, the content of the VIII-family precious metal is 0.1-10 percent by weight, in the rare earth-modified molecular sieve, the mass content of the rare earth oxide is 0.5-60.0 percent, and in the halogen-modified inorganic melting-resisting oxide, the mass content of the halogen is 0.1-20.0 percent. Compared with the prior art, the catalyst is especially suitable for a hydroprocessing process of lubricating oil distillate, and has the characteristics of high yield of a target product, low flow point and high viscosity index.