The purpose of the present paper consists of two points. First, it is to show how the internal structure and the “inner logic” of science as a value sphere are formed in Max Weber’s theory. Then, relying on logical-methodological foundations proposed by Weber, the second point is to identify how the action carried out by scientists in a “vocation” mode in a situation of “value polytheism” is realized within science. Analyzing the content of recent discussions about the empirical validity and character of Weber’s argumentation in one of his central works, The Protestant Ethics and the Spirit of Capitalism, as well as about the autonomy and conceptual boundaries of Weber’s science, we draw a line of reasoning as follows. Firstly, we trace the changing of the methodological role of values in general, and the value of truth, in particular, in the “sciences of culture” in connection with the transition from the transcendental solution of Heinrich Rickert to Weber’s “value polytheism”. Secondly, we analyze how the relationship between Weber’s science, progress, and rationalization is structured. Thirdly, we explicate the mode of “vocation” in science, relying on the logical-methodological foundations proposed by Weber. Fourthly, we identify the development of Weber’s idea of the value autonomy of science. It is shown that Weber rejects the criterion of truth’s universality proposed by Rickert’s logical solution. However, the construction of ideal-typical concepts and the mechanics of “cognitive interest” described by Weber allows scientists to separate extra-scientific pragmatics from the scientific research itself. The progress of the “sciences of culture” for Weber is the differentiation and the emergence of new research approaches and the refinement of concepts. At the same time, science is not teleologically connected with “progress in general” and the rationalizing world, the configuration of which is a specific historical constellation. As associated with scientific work, “gaining the clarity” turns out to be not its own goal, but a possible effect of using scientific knowledge. The mode of “vocation” in a “value polytheism” situation forces scientists to contribute to the endless scientific progress; they formulate such ideal-types and causal explanations that seem adequate and sufficient from the point of view of their cognitive interests. The stability of science’s boundaries and its value autonomy are formed in Weber’s theory gradually; epistemological studies and the implementation of his sociology of the religion research “programme” make the difference between vocations in science and politics clear.