Introduction: Quadriceps muscle atrophy and quality loss, defined as an increased ratio of intramuscular fat and/or connective tissue, are often observed especially in the paretic limb of post-stroke patients. This study was performed to examine the relationship of quadriceps muscle thickness (MT) with muscle echo intensity (EI) and the severity of motor paralysis after stroke. Methods: Thirty-six hemiparetic subacute post-stroke patients were enrolled. We examined the MT (index of muscle quantity) and the EI (index of muscle quality) at the anterior mid-thigh in both limbs. We also assessed the Brunnstrom stage (BR stage), subcutaneous adipose tissue thickness, time since stroke, age, body weight, sex, number of medications, and nutritional and inflammation status. Results: The MT in the paretic limb was explained by the BR stage (β = –0.26, p < 0.01), body weight (β = 0.68, p < 0.01), and serum albumin (β = 0.34, p < 0.01), with an adjusted R2 of 0.81. The MT in the non-paretic limb was explained by the muscle EI (β = –0.55, p < 0.01) and age (β = –0.40, p < 0.01), with an adjusted R2 of 0.69. The muscle EI was explained by the MT in the paretic limb (β = –0.34, p < 0.01) and non-paretic limb (β = –0.69, p < 0.01). Conclusions: Our results suggest that motor paralysis, aging, and malnutrition contribute to quadriceps atrophy in post-stroke patients. Moreover, a potential countermeasure to diminish muscle quality loss is maintenance of muscle quantity.