This paper modifies the Farnes’ unifying theory of dark energy and dark matter which are negative-mass, created continuously from the negative-mass universe in the positive-negative mass universe pair. The first modification explains that observed dark energy is 68.6%, greater than 50% for the symmetrical positive-negative mass universe pair. This paper starts with the proposed positive-negative-mass 11D universe pair (without kinetic energy) which is transformed into the positive-negative mass 10D universe pair and the external dual gravities as in the Randall–Sundrum model, resulting in the four equal and separate universes consisting of the positive-mass 10D universe, the positive-mass massive external gravity, the negative-mass 10D universe, and the negative-mass massive external gravity. The positive-mass 10D universe is transformed into 4D universe (home universe) with kinetic energy through the inflation and the Big Bang to create positive-mass dark matter which is five times of positive-mass baryonic matter. The other three universes without kinetic energy oscillate between 10D and 10D through 4D, resulting in the hidden universes when D > 4 and dark energy when D = 4, which is created continuously to our 4D home universe with the maximum dark energy = ¾ = 75%. In the second modification to explain dark matter in the CMB, dark matter initially is not repulsive. The condensed baryonic gas at the critical surface density induces dark matter repulsive force to transform dark matter in the region into repulsive dark matter repulsing one another. The calculated percentages of dark energy, dark matter, and baryonic matter are 68.6 (as an input from the observation). 26, and 5.2, respectively, in agreement with observed 68.6, 26.5, and 4.9, respectively, and dark energy started in 4.33 billion years ago in agreement with the observed 4.71  0.98 billion years ago. In conclusion, the modified Farnes’ unifying theory reinterprets the Farnes’ equations, and is a unifying theory of dark energy, dark matter, and baryonic matter in the positive-negative mass universe pair. The unifying theory explains protogalaxy and galaxy evolutions in agreement with the observations.