The traffic situation of highway work zone during discrete periods was analyzed. By dispersing the work periods, the relationships between the capacities of work zones and user costs during different discrete periods were compared, and the calculation models of user costs during corresponding periods were set up. The uncertain factors of user cost for highway work zone were analyzed. Based on the probability distributions of uncertain factors, the fluctuation scope of user cost was predicted by using Monte Carlo simulation and verified by the example of Qinglian Highway. Calculation result indicates by using the proposed model, the average user cost under the day-time work scheme is 193 148 021 yuan, and the maximum and minimum costs are 466 820 060, 117 342 849 yuan respectively. The average user cost under the night-time work scheme is 1 795 047 yuan, and the maximum and minimum costs are 3 443 468, 1 417 274 yuan respectively. It is found that the application of proposed model can show the influences of uncertain factors well.