A remarkably rich variety of nanophase-separated structures and various order-order transitions are observed in a series of low-molecular weight (MW) rod-coil block copolymers (BCPs) with the rod blocks of different lengths (L-Rod's). The rod-coil diblock copolymer studied herein is poly(dimethylsiloxane)-b-poly{2,5-bis[(4-methoxyphenyl)oxycarbonyl]styrene} (PDMS-b-PMPCS), in which PMPCS is a rod-like polymer and exhibits an MW-dependent liquid crystalline (LC) phase behavior. When the polymerization degree of the PMPCS rod block (N-Rod) is less than 32 (L-Rod < 8 nm), the PMPCS block is always amorphous in the entire temperature range. And the corresponding PDMS-b-PMPCS BCPs with N-Rod from 11 to 29 and the volume fraction of the PMPCS rod (f(Rod)) from 43% to 67% self-assemble into various equilibrium nanostructures after annealed at temperatures above the glass transition temperatures of the PMPCS blocks. When N-Rod = 11 and f(Rod) = 43%, the BCP forms a lamellar structure (LAM); when N-Rod = 15 and f(Rod) = 51%, the BCP forms a double gyriod structure (GYR) ; when N-Rod = 20 and f(Rod) = 57%, the BCP forms a GYR structure after annealed below 180 degrees C and transforms to the Fddd structure after annealed above 180 degrees C; when N-Rod = 29 and f(Rod) = 67%, the nanostructure of the BCP after annealed below 180 degrees C is hexagonally packed cylinders (HEX) and changes to a body centered cubic structure (BCC) after annealed above 180 degrees C. When N-Rod > 32 (L-Rod > 8 nm), the PMPCS rod block is amorphous at low temperatures and transforms to a stable columnar LC phase after annealed at high temperatures. Correspondingly, the PDMS-b-PMPCS BCP with N-Rod = 44 and f(Rod) = 75% forms a HEX structure after annealed at lower temperatures at which the PMPCS block is amorphous, and the nanostructure transforms to LAM after the sample is annealed at higher temperatures at which the PMPCS block enters into the LC phase. Therefore, only by a small change of the rod length in the low-MW PDMS-b-PMPCS rod-coil BCPs, various nanostructures including LAM, GYR, Fddd, HEX, and BCC are obtained. In addition, by increasing annealing temperatures, GYR-to-Fddd and HEX-to-BCC transitions are observed in the BCPs with the amorphous PMPCS, and a HEX-to-LAM transition occurs in the BCP when the LC PMPCS block undergoes an isotropic-to-LC phase transformation.