Health-related physical fitness reduces the risk of chronic disease, promotes quality of life, and has enormous economic benefits considering the global health care costs resulting from obesity. However, relatively limited information is available regarding the dose–response relationship between scientific physical fitness and obesity risk. This study aimed to determine the associations of scientific physical fitness with body mass index (BMI) distribution and overweight/obesity risk among adults aged 23–64 years in Taiwan. We conducted a cross-sectional study and reviewed data derived from the Scientific Physical Fitness Testing Program, Sports Administration, Ministry of Education, Taiwan. Responses from 16,939 participants from the database (7761 men and 9178 women, aged 23–64 years) were collected in this study. Each participant completed a series of scientific physical fitness measurements, including cardiorespiratory fitness (3 min progressive knee-up and step [3MPKS] test), muscular fitness (hand grip strength), and flexibility (sit-and-reach test). Anthropometric measurements included body height, weight, and BMI. The quartiles of scientific physical fitness results were identified as the dependent variable in the multiple linear and multiple logistic regression analysis to determine the associations of the scientific physical fitness measurements with BMI distribution and overweight/obesity risk, as well as the dose–response relationship. The 3MPKS test was significantly associated with BMI (quartile 1 (Q1): β = 1.900; quartile 2 (Q2): β = 1.594; quartile 3 (Q3): β = 1.079 for men, and Q1: β = 1.454; Q2: β = 0.882; Q3: β = 0.555 for women), overweight (Q1: odds ratio (OR) = 2.117; Q2: OR = 2.056; Q3: OR = 2.063 for men, and Q1: OR = 3.036; Q2: OR = 2.542; Q3: OR = 1.959 for women), and obesity (Q1: OR = 6.530; Q2: OR = 5.747; Q3: OR = 3.557 for men, and Q1: OR = 3.238; Q2: OR = 1.431 for women) risk compared with quartile 4 (Q4) as the reference group with a dose–response relationship. In addition, relative hand grip strength was significantly associated with BMI (Q2: β = −0.922; Q3: β = −1.865; Q4: β = −3.108 for men, and Q2: β = −1.309; Q3: β = −2.161; Q4: β = −2.759 for women), overweight (Q2: OR = 0.806; Q3: OR = 0.697; Q4: OR = 0.278 for men, and Q2: OR = 0.667; Q3: OR = 0.398; Q4: OR = 0.228 for women), and obesity (Q1: OR = 0.528; Q2: OR = 0.206; Q3: OR = 0.049 for men, and Q1: OR = 0.351; Q2: OR = 0.129; Q3: OR = 0.051 for women) risk compared with Q1 as the reference group with a dose–response relationship. Higher levels of performance of the 3MPKS and relative grip strength tests were associated with lower BMI and overweight/obesity risk in both sexes. However, the sit-and-reach test was only partially related to BMI and overweight/obesity risk in both sexes. Cardiorespiratory fitness and muscular fitness were effective predictors of BMI distribution and overweight/obesity risk in Taiwanese adults.