Internationalization of the world trade and severe competition for the position in global value chains stimulate countries all over the world to create special economic zones (SEZ). For the Russian Far East, the SEZ are the major element of fostering industrial growth and overall economic development. There are Free Port of Vladivostok, Territories of Advanced Economic Development and other development programs created to ensure inflow of investors into the economy of the macro-region. The state offers both tax deductions for up to 10 years and direct budget expenditures for creating infrastructure for the future project sites. Natural consequence of that is the problem of very different financial efficiency of potential projects and dire need to sort or filter those projects that will, probably, be mutually beneficial both for investor and for the state budget from those that, again probably, will benefit only one party or even fail for both. We started from applying standard mechanisms of project evaluation, based on sum of the discounted cash flows comparing to discounted investments, and then enrich it with instruments of working with probable events to make it more flexible. Then based on real-options approach, we show an anticipated cash-flow as the representation of project’s efficiency and create strategy matrix for private and public parties of the cooperation.