This manuscript focuses on the results of a project study on the field programmable gate array (FPGA) and modular based microcomputer architecture design for improving the teaching and learning effectiveness in computer organization course and similar courses. The design mentioned in this manuscript is a unique system allowing to students to directly write their program and/or include their own designs. The main objective of this study is to improve the teaching effectiveness in the computer organization course at graduate level via hands-on learning. The goal of the project is to encourage students to create their unique microcomputer designs since this design has modular structure and the fundamental elements which a simple computer has. Also it is to make appropriate modifications using students' concerns and the results of project study for computer architecture and organization course for next semesters. To evaluate the improvement of the teaching and learning effectiveness, the students enrolled in the computer organization course in computer engineering department are divided into two groups. A student survey is conducted to provide students with an opportunity to have their views about this methodology at computer organization course. The results of the survey acquired with the probability density distribution function reveal the effectiveness of this methodology with FPGA development environment.