Breaking the convention of the "self-interest" hypothesis， we introduce the fairness preference of agent into the contract of risk compensation of science and technology insurance，and study the effect of fairness preference and risk aversion to the contract under the principle-agent framework. The results show that the marginal incentive coefficients increase with the level of fairness preference and the degree of government risk aversion increases，but decreases with the increase of degree of the insurance company risk aversion. When the degree of the risk aversion is moderate，fairness preference will remarkably add marginal compensation rate.