Enhancing maize lodging resistance with plant growth retardants (PGRs) is common in maize production. However, the underlying mechanisms of yield formation as affected by PGRs are still poorly understood. A field experiment contained PGR application (a mixture of ethephon and cycocel, EC) with normal (T1) and double (T2) doses and water control (CK) was conducted at four maize plant densities (4.5, 6.0, 7.5, and 9.0 plants m−2) in 2020 and 2021. In this two-year study, the grain yield and kernel number per ear (KNE) of EC treatments were reduced by 4.8–9.0% and 3.3–12.2%, respectively, compared with CK under densities of 4.5, 6.0, and 7.5 plants m−2 without lodging. However, under the density of 9.0 plants m−2, EC treatments had no pronounced effects on grain yield and yield components. Across all densities, EC significantly decreased the leaf area index (LAI), and the lowest LAI was recorded in T2. The concentrations of nonstructural carbohydrates (NSCs; starch and soluble sugar) in the stem were significantly decreased by 9.9–10.2% in T2 averaged all densities. The sucrose and starch concentrations in grains also declined in the EC treatments. The key enzymes (cell wall acid invertase, sucrose synthase, and adenosine diphosphate pyrophosphorylase) and grain polyamine concentrations showed a slight downward trend under EC treatments compared to CK. NSCs in stems and grains, kernel enzyme activities, and polyamines in grains presented significant positive correlations with KNE. Additionally, structural carbohydrate (SC; including cellulose, hemicellulose, and lignin) concentrations in stems were improved with enhanced lodging resistance by spraying EC. Significant negative relationships were observed between SC with kernel number m-2 (KNM) and yield, suggesting that improved SC in stems might affect the availability of NSCs for kernel set. Although the lowest kernel weight and KNE were obtained at 9.0 plant m−2, relatively high LAI still ensured high KNM and high yield. Collectively, EC treatment increased SC in stems, enhanced lodging resistance of maize and reduced NSC availability for kernels, ultimately presenting adverse effects on maize kernel number and yield under relative low density.