Tuning polyurethane (PU) properties by changing isocyanate monomers is interesting. However, the relationship between the diisocyanate structure and the protective properties of PUs remains unclear. In this paper, two-component cross-linked PUs were synthesized from two aromatic diisocyanates, one linear aliphatic diisocyanate and one alicyclic diisocyanate with the same fluorinated polyacrylate copolymer, and the effects of diisocyanate structure on the adsorption and permeation behaviors of dimethyl methylphosphonate (DMMP, a nerve agent simulant) and 2-chloroethyl ethyl sulfide (CEES, a mustard simulant) were investigated. It was found that for the same PU, the retention of DMMP was greater than that of CEES, but on the contrary, the diffusion coefficient of DMMP was less than that of CEES. For the different PUs, the structure of diisocyanate had a great effect on the protective properties of the PUs. Compared with the aromatic PU and the linear aliphatic PU, the alicyclic PU has the lowest surface adsorption capacity and internal retention of DMMP and CEES, which should be due to its much higher glass transition temperature (T g ), weaker intermolecular interaction with DMMP or CEES, smaller free volume pores, lower degree of microphase separation, and higher surficial fluorine content. Therefore, the alicyclic PU may be the best candidate as a protective topcoat PU material.