The invention discloses a bio-based alkylthiophosphoric acid or a derivative thereof, a preparation method and an application thereof. This bio-based alkyl phosphorothioate has a structure shown in formula (I): where R 1 , R 2 , at least one of X, Y, Z, W, M from bio-based raw materials; R 1 , R 2 Independently be a hydrocarbon group, a hydroxyl group, a carbonyl group or a heteroatom; and at least one of X, Y, Z, W contains a sulfur atom, and the rest are arbitrarily selected from O, S atoms; and M is H or another one having the formula (I) Derivative groups of molecules of the shown structure. In the synthesis process of the bio-based thiophosphoric acid or its derivatives of the present invention, at least one raw material is derived from bio-based raw materials, that is, natural and renewable raw materials, which have the advantages of greenness, environmental friendliness, renewable raw materials, and energy saving. It can be widely used in the fields of lubricating oil, grease, mine flotation agent, pesticide, flame retardant and rubber accelerator.