The aim of this paper is to develop a methodology for determining the size of the unified land tax in agriculture based on the results of the economic assessment of agricultural land to form the foundation of a new effective system of macroeconomic instruments for state regulation of the innovative development of the agro-industrial complex of the Republic of Kazakhstan. There were used gatherings of facts and summaries, induction and deduction, analysis and synthesis, historical and logical, normative, comparison, index and modeling methods in the research. The article provides an overview of various scholarly perspectives on the challenges and strategies for improving the tax system. The base rates of the unified land tax per hectare of arable land have been calculated to establish equal conditions for all land users. This unified land tax rate is expected to encourage the efficient utilization of land resources and enable the optimization of production structure. The article addresses avenues for improving water management relations in agriculture, aimed at fostering a shared interest and creating incentives for adopting innovative technologies in both agriculture and the water management sector. An essential condition for achieving the effective functioning of Kazakhstan’s agro-industrial complex is its transformation to an innovative development model. This necessitates the development and application of a new system of macroeconomic tools for its implementation, aimed at creating a favorable environment for entrepreneurial development.