The article highlights the features of management innovation companies based business cost indicators. The estimation of the value of business cost indicators constituting the three approaches, namely, market, cost and income. The necessity to use the highly-qualified labour resources, the last scientific inventions and researches, as well as the newest innovation technologies is emphasized. The innovation model of development should be used at the enterprise for this purpose. For the effective management of innovation companies it is necessary to control the situation on the market and execute management on the basis of indicators of the business cost. The management of the innovation companies on the basis of the business cost includes: management of the organizational capital, management of the intellectual capital, and management of information capital. As a result, the innovation company receives the wide client base, competitive prices, the high level of service, the high quality of the offered innovation services, the availability of the own innovation developments and highly-skilled staff.