The present invention includes a rubber composition containing a modified diene polymer having a group represented by Formula (I) below and a group represented by Formula (II) below, and silica; and a modified diene polymer and a production method thereof. In Formula (I), X1 represents at least one selected from the group consisting of a nitrogen atom, an oxygen atom, and a sulfur atom, X3 represents a hydrocarbon group, n3 represents from 0 to 4, and X2 represents at least one selected from the group consisting of sulfone-based protecting groups, carbamate-based protecting groups, and —(R—O)n4—H. In Formula (II), R1-1 represents a divalent hydrocarbon group, R1-2 and R1-3 each independently represent a monovalent hydrocarbon group, m1 is from 1 to 3, m2 is from 0 to 2, m1+m2 is 3, and R1-4 represents a hydrogen atom or a hydrocarbon group.