The investment behaviors of Medical Operation Funds are conservative. Most of the capital is deposited in banking. In recent years, the interest rate of banking has declined dramatically. This affected the return rates of Medical Operation Funds. Therefore, these funds seem need to invest in other asset classes to raise returns. This paper applies Markowitz mean-variance portfolio model to build up two asset allocation models. Stocks investment is not allowed in model A, whereas model B permits investment in stocks markets. According to comparison of these two models, we find that investing small proportion of capital in stocks is helpful to diverse risk and improve return rate. However, the risk of the portfolio increase speedily when stock investment weight over 4$. In addition, this article uses Variance-Covariance Method and Monte Carlo simulation to evaluate the VAR of Medical Operation Funds. Finally, we proposed several suggestions relating to funds management regulations and asset allocation.